It's one thing for a church to fly an Obama or McCain flag, which I think crosses a line, not just Jefferson's wall-between-church-and-state line, but also one based in Scripture. However, given how queer people are marginalized in mainstream society, I think a rainbow flag, or other overt symbol of welcome, does not cross a line. It only seems political because gay marriage laws are being fought over and are hugely partisan. Being welcoming to queer people goes far far beyond the narrow question of legalizing same-sex marriage.