It's more general than "why are you awake?", which means roughly "why, at this specific time, are you awake?" "What keeps you up?" could be understood as "what keeps you awake at night (all nights)?", or "why aren't you getting much sleep?" "What is keeping you up?", however, means very much the same thing as "why are you awake?" Hopefully that helps.

It means "When you stay awake, what's the cause?" (Is it work, worry, TV, etc?) You could rephrase it as "What keeps you from falling asleep?" If you want to talk about right now (instead of just speaking in general terms), you can ask "Why are you still awake?" or "What's keeping you up?" I hope this helps you. ;)