The "FR is inherently anti-Catholic" argument was openly waged with the moderators a couple of years back. IIRC, the crux of the argument was that FR's posting rules are biased towards Protestant iconoclasm (2 Corinthians 10:5). Their proposal was that the Religion Forum should re-write the posting rules to enforce respect for Catholic iconography and ideas. The practical upshot would be that every thread would effectively become a "Catholic Devotional" thread.
Needless to say, the moderators rejected the idea.
I believe we have very wise Moderators!