I'm reading it, and from what I can tell she is being criticized for her politics. What's happening, according to the article, is that conservative leaning media and religious groups are framing those questions as anti-Catholic. It's a nice time honored political move of screaming "discrimination!" whenever people speak badly about you. It might fire up some demographics, but I don't see it.

The complaints about her have been purely about her political views and never about her religion directly.