It's more of a southern thing than a Republican thing. You won't see a native northerner (Rep or Dem) flying the Stars and Bars, and you'll see both Rep and Dem southerners who support that symbol.
While I do associate the Confederacy with slavery, I don't think folks flying the Stars and Bars today are aiming at reestablishing slavery. That said, it still conjures bad mental imagery when you think about every thing it stood for.
For me, however, the bigger issue is that the Stars and Bars are "Anti-American". I fully support any State's right to secede from the Union (controversial as that may be), but I don't think you can claim you are proud to be in the USA, while displaying or championing a Confederate banner. "Hate" may be a strong word to use, but there has to be a good deal of emotion behind the decision to secede, so I don't think it's much of stretch to say that anyone who flies and champions a Confederate Banner is saying, "I hate the U.S. and wish my State could no longer be a part of it". And while I have stated I support anyone's right to do that, I also can admit that I don't care to have them in my country, and they are not someone I would choose to associate with.