How does an online poker site protect its customers from collaboration?

If by collaboration you mean 2 or more players working together trough instant messaging services or voice services the answer is the following:

Online Poker Sites automatically keep record of the players you are playing against and how frequent. Poker sites are able of tracking multiple stats against a certain opponent. Once they notice that 2 players are working together in order to gain money in an unfair way, the poker site will often warn them first and/or completely terminate their account depending on how grave the situation was.

This system works partially automatic and part manually, a computer will detect patterns against certain players and then people will analyze the data given by the computer. If these notice and/or are having serious suspicion of collaboration, they will issue a warning and/or terminate a players account.

The way these bots are picking up these patterns is pretty much by analyzing your playing style against certain opponents, online time etc and combining all of these together.

Of course the actions taken against these people may differ from one online poker room to another, best to read the Terms of Use of the poker site you are playing on regarding this matter.