Taking what you've stated in the OP and what btc-e.com does, I think it would be a good idea to charge a small trade fee 0.1% or less and charge a withdrawal fee as well.
Understandably, brokers have to make a profit from somewhere too.
I would also charge a licencing fee for anybody who wants to use the API as developers using these API's are the ones that place the most strain on the system. Thinking out aloud, free for basic use would be a good idea but then $10 or so a month for trade placing will put off kids running 1 cent scalping bots.
An API fee is definitely another way to go. Maybe as well as or instead of some of the other measures.