I view Captain America as political in the same way as Superman is political. Both characters are used in their respective universes to represent American values, whatever that may be to a writer at the time.
The problem with politics these days is exactly what you describe in your second sentence. There is a nasty, take no prisoners, with us or against us sentiment in most of it. Cap shouldn't be that, and I certainly hope he doesn't become a standard-bearer for the anti-Trumpers out there.