I don't agree with what Bob says, although I totally agree with where he's coming from. Marvel Studios does give creative freedom to their directors, but it is creative freedom in a framework which Marvel controls tightly.
They approach it much like how they approach comics, where individual artists and writers are free to come up with good ideas and to inject their own personal styles into the designs and the narrative flow they're working on, but at the same time they have to stay consistent to the overall Marvel Universe, and there are specific requests made include or exclude certain elements as Marvel sees fit for the given story of a movie.
What this means is that some directors who are more familiar with working within frameworks like this will be more capable of flexing their creative muscles than others who are not. It's also possible that some directors sign on to such projects without wanting to do anything particular creative of their own on the movie, just cashing a paycheck.
I do not agree for a moment that if a director has something creative to contribute to a project in a good way, that Marvel Studios will actually work against him and just want him to "follow instructions" instead. A lot of it is about how you collaborate, and some people are better at doing it than others. If Marvel really wants nothing but yes-man directors, there are a lot more choices for them. Instead they have been more actively looking for directors who in fact fit the tone of the movies they are looking to make.
Thor and Captain America are actually great examples where the directors they picked were selected to bring a specific creative style to the movies which both directors had done before, but within the framework of the Marvel Universe.