Michael O'Loughlin's entire HuffPo piece, "The Catholic Church Isn't Anti-Gay, but Are Its Bishops?", is based on a rather foolish conflation. What he seems to be trying to say is that the average self- described Catholic isn't anti-gay. On that point I agree. The majority of people who identify as Catholic are not homophobic and don't seem to have an interest in telling others how they should live their lives. That is not the same thing. The average Catholic has no power or influence when it come to either the church hierarchy or the church's doctrines.
The Catholic Church as an organized religion is indisputably anti-gay. The hierarchy and doctrines still insist that homosexuality is a sin and that equal rights for gays (including but not limited to gay marriage) is unacceptable. That is the church's official stance and it routinely meddles in politics to enforce that view. Anyone who cannot see that being anti-gay is a complete moron.