Here is how I see it:
Phil Robertson is free to have his moronic and archaic views about gays and is free to say his hurtful and stupid comments because he is a person with an opinion (guaranteed by the constitution).
A&E is free to have their views about gays and their views about how they do not agree with the hurtful and stupid comments made by Phil Robertson and they are free to act upon this because they too have the same freedom of speech rights as Robertson has. A&E for all purposes intended is a person under the constitution and thus have a constitutional right to free speech as well. And if you are of that opinion that the words of Robertson are totally unacceptable for you as a person/company, you have the right to not cooperate with such a person anymore.
Also, Phil Robertson did not only make anti-gay comments but he also made moronic comments about blacks, the moron and chief of the Ducks stated:
“
I never, with my eyes, saw the mistreatment of any black person. Not once. Where we lived was all farmers. The blacks worked for the farmers. I hoed cotton with them. I’m with the blacks, because we’re white trash. We’re going across the field.... They’re singing and happy. I never heard one of them, one black person, say, ‘I tell you what: These doggone white people’—not a word!... Pre-entitlement, pre-welfare, you say: Were they happy? They were godly; they were happy; no one was singing the blues.”
Phil Robertson On Racism In GQ Article - Business Insider
Sure, in the segregated period of the United States blacks were happy working the fields and singing. And the Blues according to the Duckster must have taken place after they were "entitled", when they were happy slaving away on the fields not having real civil rights.