Thanks Randy, and no problem, amgenpharm.
If you're getting rythmic rub on and off the trainer, there are two obvious things to consider (pardon the rehash). One is that your wheel and/or brakes are simply sitting out of alignment. Even if they're only a bit out of alignment, the uneven-ness can be magnified by frame flex as you pedal. Unclamp the quick-release, and re-clamp it, taking care to see that the rim is centered between the brake pads as you push the skewer lever down. Eyeball the brakes and make sure they aren't sitting crooked either; sometimes re-centering the brakes makes all the difference.
Looking good? Now spin the wheel, and take note of whether the rim wobbles in relation to the pads as it goes around.
If that's the case, either your skewer is tweaked (drop $7 and buy a new pretty one), or your wheel has, in fact, gone out of true.
In case you're not sure what it means, wheel true-ness denotes that the hub, spokes, and rim are aligned and tensioned such that the hub is at the precise center of the wheel, the rim is a near-perfect circle, and that the whole assembly spins on a plane perpendicular to the axis. Most wheels lose their true-ness from time to time. Sometimes it's just general wear, and other times, it's a particular event -- a nasty encounter with a pothole, for instance.
Truing most wheels is something you can learn to do yourself, though it's a project which takes lots of practice, a chunk of time if you're not an ace at it, and some tools. Your local shop can probably do it in a mater of minutes (I take my untrue wheels to the shop). The process involves different techniques, but usually is accomplished by adjusting spoke tension here and there.
Ok, good luck. Take it to a shop and see what they say.