A damaged reputation is not always the death nail of a company, but it can be especially if there are other factors involved. Certainly Exxon is an example of what you're saying, though I'm not sure how you can put Microsoft up there with Exxon. I'm not even sure that Microsoft has a bad reputation. Sure, some people might have bought into that "I'm a Mac" schlock, but you could say that marketing campaign has pretty much become ubiquitous and a sign of all things pretentious. In fact, Harris polls show that Microsoft's reputation is actually ranked pretty high in relation to other companies, including Apple. I'm not in any way trying to say that Microsoft's reputation is spotless and that it didn't take hits with Vista, but comparing Windows Vista to the Exxon Valdez oil spill might be overstating things a bit.
Maybe you haven't noticed, or maybe you live in Redmond, but people complain A LOT about MS. They've been sued for billions of dollars by several major world governments. It has nothing at all to do with stupid Apple ads. WTF.
My point was rep does not=money. I hate KBR, as do a lot of people, but I help make them one of the richest companies in the world just by paying my taxes. If I don't pay my taxes I go to jail, so its irrelevant how much I hate them. I hate MS, but while I have a personal boycott against their gaming/music stuff, I can't really do much without using Windows...so they got my $35 for Win7 as well as licenses for all the computers where I work. I hate Exxon, but what am I going to do, use gasoline from a less evil oil company? There's no such thing.