For a counterexample, Facebook is professional-looking and very structured compared to MySpace, which in turn is very amateurish-feeling.
There isn't any question which is preferred.
Forums are amateurish. Stackoverflow is professional. I know where I'm going for Q&A.
I think there's a lot more to Apple's problems than professionalism vs amateurism, to the point where it is a minor point, if one at all.
I'm very wary against sayings like "the web is about amateur content." The web is about a lot of things, and while a lot of the web is about amateur content, a lot of the web is also about providing good structure, order, and execution to that content. In general, it even seems to be that the company that can put the most order unto the all of the content reaps the greatest success.