I was once told recruiters did this because they didn't want you reading the email and heading straight to the company's site to apply. If you applied directly, the recruiter was out of the loop and thus out of a commission. I suppose I _might_ be able to negotiate that commission in the form of a larger signing bonus. I doubt that's a winning strategy.

It seems like it would usually be in the best interest of the potential candidate to work through the recruiter. By having been sought out, you have an advantage. You can actually talk to a recruiter and check status of your progress, where as a web application is a black box of which you may never hear another word. At some point the recruiter is going to feel invested in you.