@Zensate Uh, no. Being compatible with secular values and ideas of human rights does not make someone or something "atheist" or a bad Catholic unless one interprets their faith in hegemonic terms (i.e. that its the Pope's or the Church's job to be intolerant).
The Catholic Church has a history, a lot of it being nasty, yet core Catholic doctrine (divine inspiration can come from many sources and be interpreted by people, uh, the person) suggests a lot of that history was totally unnecessary.
But keying on your own theme, its more likely that a religious person who can't find common ground with atheists or other religions is really just a "terrible" person.