Nate's description is pretty accurate.
The original reason was to not include the ugly merge commit that pops up. Since then, we've discovered other uses for it.
We rebase to keep the history clean and in 99.9% of cases this has been useful because we can compress PR commits into one and edit commit messages (and sometimes code) as we see necessary. The 0.1% where it's not been useful have been my topic branches where it's taken me HOURS to rebase master onto my branch. But not everything can be perfect.
Also, by clicking the merge button, it'll only merge it to one branch. More often than not, the pull requests are applied to more than one branch (master and 1-3-stable is the standard at the moment). We could ask people to submit multiple PRs, but the current workflow (rebase and cherry picking) is quicker than going through a web UI. I've also got some terminal functions to help me out with things.
I hope that explains it for you.