2007 Honda rebel won't start lights don't work?

So I left the key turned for a few hours and the battery died. I got it charged and checked and everything shows as being good. My roommate tried jump starting it when I went to work so I don't know if that hurt something. All the fuses are good. However when I turn the key the bikes lights don't come on, nothing works. I can put it in first and the get a running start to crank it by popping the clutch. That works for day time riding, but at night the lights are dim. Any ideas?

If the battery is good, then something got hosed when it was jump started.
Unless you're a gear head, seems like you need to go seek professional help at this point.

First, you should NEVER try jump starting a motorcycle with a car battery. I assume that's what your roomie did. Second, once you let the battery die, they frequently need replacing after that. Third, you may have damaged the regulator/rectifier unit. Try measuring voltage at the battery with the engine running. You said you can push start it. You should see 14 to 14.5 or so volts with the engine running at a couple thousand rpm. If you don't, regulator/rectifier is bad or stator is bad or associated wiring is bad. If you do, replace the battery.

By leaving the key on, the battery drained down to zero.
The battery is not even strong enough to turn on the lights.
While the engine is running, the charging system is doing all it can to try and charge the dead battery and has nothing left to make the lights bright enough.
Replace the battery.