Outside of the Northeast, you can find people who believe that Catholics are not true Christians everywhere. The KKK was anti-Catholic, as well as anti-Jew and anti-Black. Many of the born again types I ran into in Los Angeles, including a Korean presbyterian, had this belief about Catholics.
As with other forms of prejudice, many believe it without being motivated to act on their beliefs in any way, whereas a few take it to extremes.
You know why that is? Most people think you worship a mortal - Mary. Everything is Mary, not Christ. There's Mary's beads, statues, prayers, ornaments of Mary, but very little has to do with the one who bought you.
I always thought the Catholics made Mary their Goddess. That's all I ever saw. If one listens closely, they'll notice Mary is used to get to Christ in the end.