I think O'Reilly's arguing on the right side for the wrong reasons. People most certainly can and should protest a business if they feel it is doing something wrong.
The real issue is not whether it's wrong to protest a "business decision". The real issue is whether being gay has anything to do with morality in the first place. The people who are calling for Ellen to be fired believe it does, and the real answer is that that is wrong, not that business decisions are somehow exempt from protest.
He might be playing a little misdirection game here. Notice how he compares this to calls for him to be fired. (For me, Glenn Beck and Pat Buchanan came to mind.) He claims those are also wrong. I think he wants to be able to shoot down any attacks on him by saying "Hey, I defended the liberal side when it came to a gay person. Aren't you being just as bad as OneMillionMoms?"
I'll give O'Reilly more credit the day he stops calling homosexuality a "lifestyle", which is code for "It has moral implications."
I did enjoy his mocking the OneMillionMoms for declining to appear on the show. And the fact remains that he is defending Ellen Degeneres, for which she's rightly thanked him.
See also "Ellen Addresses Her JCPenney Critics".
[EDIT: Switched the second and third paragraphs.]