Ok, here's the thing; just because you "answer honestly" doesn't automatically end any criticism of what you have said. For example, if Miss Prejean had been asked, "Barack Obama has been elected President of the United States. Do you really think that the country can trust an African-American in the nation's highest office?" And let's say Miss Prejean answered, "my personal view is that black people are inferior and do not deserve the same rights as white people. I'm sorry if anyone is offended, but that's just what I believe."
The simple fact is that Miss Prejean offered an opinion about gay marriage that no matter how "sincere" or "honest" is based on intolerance and leads to the denial of civil rights for an entire group of Americans. While obviously Miss Prejean has the right to her opinion; the rest of us have a right to judge her harshly for it. And well we should. Quite simply, no one has the right to hide behind their "beliefs" when they are expressing fundamentally intolerant views.
What really surprises me in all of this is how the right has embraced a position that is usually reserved for the feel-good left: "I'm entitled to my opinion and people can't criticize me for how I feel." It's a ridiculous and untenable position, and it's a hypocritical thing for the right to embrace, regardless of the outlook of the person clinging to it.