Comapct flourescent lights are flourescent tubes, just in the form of a bulb and thus more practicle. They are perfectly fine to use with timers. I use it, along with probably thousands of others. When you have a timer, it just stops and starts the electricity flow to it. On or off. Just like when you press the button.

If you want to read more about it, take a look at wiki:
Compact fluorescent lamp - Wikipedia, the free encyclopedia