Consider three choices: (1) Big company X on Windows + .Net, (2) Big Company Y on Linux + C++, or (3) co-founding a new startup using whatever I prefer. I wouldn't fault anyone for having pre-conceived notions about the cultures prominent at these companies, would you?
His whole email could have been summed up as "you're on Windows, I don't do Windows". That's not condescending, that's his preference and HIS reason for not taking the job.
Maybe. "Rather, the same initial rejection would occur, for the same reasons; and the search for justification, afterward, would terminate at a different stopping point. [..] This might be an important thing for young businesses and new-minted consultants to keep in mind - that what your failed prospects tell you is the reason for rejection, may not make the real difference;" - http://lesswrong.com/lw/wj/is_that_your_true_rejection/
What is he supposed to add here to avoid condescension? He was asked a question, this belief drives the answer. He admits his opinions might not be fully formed ("seem arbitrary"), and claims no general truth for his opinion ("indicative to me", rather than just indicative). And he's giving his basis for preferring Unix, rather than a vague "I don't like Windows". He's actually not negative about Windows at all!