One of my pet peeves is when someone will say something like "the Catholic religion" or when Protestants and Catholics alike will use the word "Christian" when they really mean "Protestant." Catholicism is one of the three branches of Christianity (Protestantism and Orthodoxy being the other two). This chart should help illustrate the taxonomy:1, 2

|                               |                             |
Catholicism        Protestantism        Orthodoxy

Catholic or Protestant, we're all followers of Christ. When Jesus prayed for all believers in John 17: 20-26 the first thing He asked God for was that we would be one as God and Jesus are one. I know that there are many disagreements between Catholic and Protestant theology, but so many of them are shallow, and the ones that aren't shouldn't stop us from being the unified, amalgamated body of Christ.

1 - Dann's Offline Scratchpad made doing this chart a heckuva lot easier.
2 - Thanks to VT_Hawkeye and Dann for info on Orthodoxy.