Most of the larger cities in Colombia have websites where you can check times and routes:
http://www.terminaldetransporte.gov.co/destinos/
It looks like Omega has a bus to Bucaramanga with a stop in San Gil, that departs at 1am. The terminal is pretty close to the airport. Late at night, you're looking at about a 10min taxi trip. I've used the Omega service from San Gil before and it was fine. Leaving that late really limits your options, so you aren't going to have a whole lot of companies to choose from.
You can kill a few hours in the terminal no problem. There are many bars in the terminal, but I'm not sure as to what time they close. If they are still open, you could pop in a drink a few beers while you wait. The terminal is generally safe. Just keep an eye on your stuff and definitely don't let it out of your sight. There are lockers in the terminal, so if you're looking at a pretty long layover, I'd just put my things in a locker and be done with it. The airport would be ok too, but I'd just go to the terminal and hop on the first bus available.