Well, it sounds like you didn't get a flat rate bid from him. Your option is this: if he blows past his estimate you might want to start to question the billable hours and he might work with you on that, but the fact is that it looks like he's being straight with you about what he's doing, and that's a good thing from a contractor. If you seriously think he's trying to milk the contract, take a close look at what your escape clause looks like. Those things exist for a reason.
"Never attribute to malice that which can be explained by stupidity." - Hanlon's Razor