This is a confusing post by Aaronson. A commenter on that post interprets the offer to mean that Aaronson thinks the proof is almost certainly flawed, arguing that if expressing his certitude has a value of (say) $100 to Aaronson, then Aaronson believes the probability that it is correct is 1/2000. I originally read it this way as well, as did Eliezer: http://news.ycombinator.com/item?id=1587295

But then Aaronson responded by saying "If I were a Bayesian rationalist, I’m sure I’d agree with you!" and instead claims that the rationale for the $200k is that "If P≠NP has indeed been proved, my life will change so dramatically that having to pay $200,000 will be the least of it." and that "If P≠NP is proved, then to whatever extent theoretical computer science continues to exist at all, it will have a very different character."

That almost sounds like the justification for a reversed insurance bet, except of course that if the proof if wrong then Aaronson doesn't stand to gain anything. So yeah, confusing.

Bottom line, I would caution against interpreting this to mean Aaronson is betting against the proof.