Faith is believing in something without having proof of it. Faith is knowing something even though rationality does not bring one to such knowing. Faith is not inherently rational. So having faith in something does not make it true or real. If a presidential candidate has faith in something that I do not agree with, then that is solid basis for me to reject that candidate.
Tolerance is the willingness to accept and allow someone's beliefs and practices. I am willing to accept and allow Mitt Romney to be whatever flavor of believer that he would like. I am not, however, willing to give my vote to him. I tolerate his religion and I oppose his election. The two are compatible.
Last but not least, let me point out that Romney used the word "should" in his argument. Should we do everything that someone tells us we should? Should is the language of authority, telling us what to do. Should does not explain its reasons, it just tells us what is right or wrong according to the speaker of the should. To me, the word should is a huge red flag, and whenever it is used, the statement it supports will be questioned.