The song has nothing to do with flags or patriotism or religion. It is an anthem of a generation in the US that changed the country and the way it looked at civil rights.

I agree. It was anti-establishment rather than patriotic. Listening to some of Dylan's other songs from that era (e.g. Masters of War, With God On Our Side) makes it clear he was no waver of the stars and stripes.

Maybe the wording of Blowing in the Wind was deliberately vague for that reason - rightly or wrongly, he may have believed he had to be careful what he said. He may have thought that if he had been too direct in his criticisms, the US government would not have approved and might have found a way to shut him up.

(I have no evidence for these comments, it's just speculation on my part)