Apple was the underdog at a point where Microsoft got its bad image by virtue of it's monopolistic practice. I can't help but think that a lot of it is a combination of inertia and MS pissing off a sufficient subset of geeks at a point where we made up a much larger proportion of the online discourse and so could set the tone. And for at least a time, in part by virtue of MS bad reputation, a subset of geeks saw Apple as a possible saviour.
It also helps that for all of its calculated business behaviour, Apple also has a reputation for better quality that makes people want to give them passes for things MS wouldn't get a pass for.