Update 2013-01-27: I wrote an updated, and fuller, set of directions.
I recently sat down to make a few notes about following the Rivanna Trail, and thought that if I posted them here, people might find them useful. In my experience, the map the Foundation provides, and the accompanying notes, still leave you exploring various sections along the trail, trying to find the right way. All the same, I love the trail, and consider it one of the best things about living in Charlottesville. The main trail is marked with green diamonds that say RTF. There are a few trail stubs running off the main trail (or alternate routes for some sections), and these are marked with brown diamonds. The notes below attempt to guide you counter-clockwise along the trail, following the green trail, starting from the trailhead near Fontaine Research Park, and bringing you all the way back around to the trails around the O-Hill area. At that point there are many options for which trails to take, and I won't try to guide you through it - besides one little remark about the one turn that doesn't seem to be properly marked, if you are trying to follow the trail.
These notes should not be taken as authoritative or anything, though I believe them to be correct at the time of writing.
Fontaine - Sunset: The trailhead is on the east side (the side the research park is on) of 29, just north of the bypass. There is a nice large sign. Taking that trail, it isn't too far before you get out to a road again (you cross over a fence on a ladder sort of contraption at one point). You'll follow that down-hill for a short bit. The trail continues on your left (there's a sign), just after you cross the bridge. Along the trail, it isn't long before you cross a creek, and then you'll come out to a gravel road. You turn right on that road, go under a bridge, and then the road forks, and I've always gone to the left. That'll take you up a short, steepish hill, and it'll soon become a paved road - Stribling. From there, you turn right on Sunset (still paved) and you'll go down a hill. That road comes to a T, and you turn right to stay on Sunset. That road ends shortly thereafter at a little parking lot and a small creek (probably pretty dry this time of year, I'd guess). You cross the bridge, and the trail goes off to the left. If you keep going straight, instead of taking the trail, you get to the Eagle's Landing apartments.
Sunset - Azalea Park: After a while, it'll pop you out at a road, McElroy (you'll be at the end of this road). Follow the road, which loops around to the left, then take another right to get on Middleton, which quickly hits Old Lynchburg Rd. I generally turn right at that stop sign, and follow the road down to Azalea park, which'll be on your left. I think the trail literature suggests you cross Old Lynchburg, and turn right on the next road, since it's less busy (Old Lynchburg makes me nervous, it's twisty and there's not really any shoulder, and the cars go zipping by). I'm not sure where that'll take you, but it certainly heads down toward Azalea Park.
Azalea - 5th: The last time I was down at Azalea Park (early July), the grass was pretty tall and overgrown. Perhaps they've done some maintenance since then. Anyway, the trail goes kinda through Azalea park (I think there's a few ways to do this), following and eventually crossing the creek. You'll end up at a wide open space, with the creek on your left and 5th street in front of you. The trail crosses under 5th at the creek.
5th: Last I was there (early July), the section around 5th street was in bad shape (fairly essential bridge was out). I suggest, when you get to 5th street (right after going under it, if I recall, you can turn right and go up the embankment to the road), just turning right on 5th (to go north, back towards C'ville) and following the road for a while. You'll cross Harris at a light, and head down a hill. Shortly after the road starts going up again you should see a sign for the RTF on your right. It'll be just a little before a new development, which I seem to recall is called Italian Villas, or something similar.
5th - Avon: Following that trail for a little while (the creek will be on your right most of the time, but I seem to recall a crossing right before the end), you'll eventually come out at a little park - Jordan Park. Head out to the road (6th) and follow it left (the park is at the end of the road, there's only one way to go). Go just a short bit and you'll get to Palatine Ave, which you'll turn right on. That'll take you to Avon St (a somewhat busier road, you'll be at a stop sign). Turn right on Avon. Shortly after crossing the bridge, the trailhead is on your left, and it doubles back on the road (so you basically make a u-turn), and then you turn right to continue along the trail, following the creek again.
Avon - Woolen Mills: Following that trail, and the green signs for a while, you'll eventually cross under a road (Woolen Mills), and the trail continues. The creek will be on your left, and 64 off to your right. There is a fairly rocky section in here, so if the weeds are covering the trail at that point, you'll probably have to slow down a bit to do all the rock-hopping safely. Eventually, if you just stay on this trail, you'll get to a short, steep (up) gravel section, that ends at railroad tracks. You've got two options at this point, both of which involve crossing the creek. One way is to just walk through the water, the other is to cross on the railroad tracks bridge. I've always taken the bridge option, but it always makes me nervous. Some of the boards aren't in great condition and you're up kinda high. Also, I don't know if it's still in use, but I would not want to be up there when a train went by.
Bridge - Riverview: If you take the bridge option, after you cross the water you'll need to venture down the hill off to your right. The railroad tracks cross Marchant Rd, which you can take to get down the hill. It'll get you to E. Market St, where you turn right. Shortly thereafter you turn left on Riverside (at the Woolen Mills Chapel) and go down a short, steep hill, at the bottom of which is Riverview park, on your right. All these roads are paved.
Riverview - River Rd: At Riverview, you'll be following the parking lot, and there will be 2 trails. One would be if you continue straight, the other goes off to the right, heading toward the creek. You can take either, they both meet up after a short while (I generally go off to the right, I think it's just slightly longer). The trail will be a paved walkway for a few miles, and basically follows the creek (which'll be on your right), passing under route 250 at one point. Eventually you'll pop out at a field with some soccer goals set up. You can continue following the trail, or you'll see a parking lot off to your left - you can head up there and turn right on the road that's there (River Rd). If you stay on the trail, it'll go just a short bit, and then there will be signs pointing you to the left. That trail heads up a hill, then runs along a fence at a VFW building until you get to the road (River, same road), on which you'll turn right.
River and Locust: You head up the hill on River, and at the stop sign at the end of River (at the top of the hill), you turn right on Locust. That'll head down a little bit, and get to a T. You head left at the T, and then take your first little road to your right. At the end of that short little road is a sign for the RTF (kinda on the right side of the road).
Locust - Morton: From there, the trail is fairly easy to follow for a while. You'll pretty much follow the creek, and the trail is mostly well-marked. You'll cross Holmes Rd, and also go under Rio Rd (where it changes to Park St, at the traffic light with Melbourne, if you were actually on the roads). The trail continues for a while, following (and occasionally crossing) the creek. Eventually, you'll end up crossing over the creek on a concrete bridge along a hill, and you'll see a big fat pipe running along the creek on the far side. At the top of that hill is railroad tracks, but the trail doesn't go up that way. You cross the creek, and then get on the pipe, going right (it ends just off to the left). This goes through a bit of a tunnel, under those railroad tracks. After this, it's again fairly easy to follow the trail. Just keep your eye out for signs and the trail markings. You'll have a few more tunnels to go through, and a road crossing or two. At one point you go through a tunnel (under Hydraulic Rd), then a short way until some stairs, which bring you to the intersection of Hydraulic Rd. and 250. Turn right, and then after going over a bridge over the creek, the trail goes off to the left (there's a sign), down a short hill and through another tunnel (under 250)
Morton - Barracks: The trail spits you out behind some hotels on Morton Dr. You turn right on Morton, and are quickly greeted with 29/Emmet St at a light (the intersection where Bodo's Bagels is). Cross 29, and continue straight on Morton (or, what would be Morton. It might just be a driveway). Near the end of that little road you'll see a sign on your left for the RTF. That'll put you on a gravel pathway. Before too long that bit of trail ends after crossing a little bridge, and you'll see a little road basically in front of you (trees on your left, building/parking lot on your right). Go out to the road (Cedars Ct), turn left on it, and it ends at Barracks Road. The trailhead is basically straight across Barracks from there (there's a sign).
Barracks - Ivy: One you get on the trail, after crossing Barracks, the trail is again pretty easy to follow for a while. Just keep following the little green signs. You'll cross a road (N. Grounds Connector, the 250/29 bypass is off to the right) after going up a steepish hill, but the trail pretty much just keeps going there. At the next road you get to (Old Ivy), there's no indication where to go. You turn left on Old Ivy, but then a quick right into a parking lot (I can't remember what for right now, I think it says something about books, or library, or special collections). Going along that parking lot, there'll be a building on your left, and at the end of the parking lot you'll see a road (Ivy) and railroad tracks, and the way to get to them (it's easy, just going through the grass, and crossing the railroad tracks). Cross Ivy (you'll be at a light, basically), and there's a little fire station there, and a sign for the trail.
O-Hill: You're now back at the O-Hill area, and there are many, many trails in that area. Some of them dump you out at roads besides Fontaine. If you are trying to follow the marked green trail, the last time I ran it there was only one junction (that I recall) at which I couldn't tell, by the signs, which way to go. It's at a little bridge, and you can either go straight then right, or left which will take you up a (big) hill. If you take the straight/right option, you'll start seeing green signs again before too long. If you go left, and up the big hill... you'll have some fun finding lots of trails and seeing what roads they come out at :)
So there you have it. I hope these helped, or at the very least, didn't lead you astray anywhere. Perhaps someday I'll wander around the trail with a camera, to make it easier to follow the descriptions above. Until then, I suggest taking a sense of adventure with you, at least your first time out. It took me some exploring to find my way around the trail. My favorite section is from Riverview park back to Fontaine, which I've done many times. The other bit I don't enjoy as much, don't do as frequently, and therefore have slightly lesser memory for. If you've got suggestions, or better descriptions, for any parts of the trail, feel free to leave a comment.