I mean, if you are going to ding Microsoft for that, you might as well ding Google and Facebook as well. Heck, only Amazon and some smaller companies have true urban campuses.
I really like working at a Google satellite office but I would absolutely never work in the Mountain View campus for similar reasons.
I found it easier to get into a Google satellite office while Microsoft wanted me to work on the main campus.
It depends on when you want to commute, if you want to fight it out 7-9:30/4:30-6:30 with rush hour traffic, then ya, it might take 90 minutes (wait, no, it would never actually take 90 minutes unless you were commuting from north or south of Seattle....or maybe West Seattle, I guess you are exaggerating a bit here). If you travel off peak, its like 20 minutes between OTC and downtown by bus.
That being said, if I had to choose between a toxic work environment with a great location and a great work environment with a crappy location, I would probably pick the latter for my own sanity (best to have both, though).
Regarding the ninety minute commute it was frequently Thursdays to where I lived in Belltown that would consistently be 70-90 minutes. I ended up staying late at work to avoid it, which didn't help my enjoyment much.