Well take a look at who the fundamentalist Republicans voted for in the 2012 primary...Rick Santorum.
...after they'd exhausted every other conceivable alternative to Mitt Romney.
Right, but the obvious reason why isn't because Santorum was Catholic, but because he was clearly a terrible candidate. If they were so opposed to Catholics they would've never considered him and would've decided to just settle on Bachmann or someone, sure an awful candidate, but not really much worse than Santorum all things considered.
But besides that, let's consider that the SPEAKER OF THE HOUSE is a Republican Catholic. So that alone makes it pretty absurd to argue that the Republican Party is anti-Catholic, or even that all Republicans are Protestant.
The Republican Party isn't anti-Catholic. However, there are some Evangelicals in it who are, certainly a minority.