Here's my take on the issue.
I have no problem with Phil Robertson holding or articulating his beliefs. They're his beliefs and he has every right to them. At the same time, not everyone likes his beliefs, and those people also have the right to hold and articulate their beliefs. Free speech goes both ways.
A&E, as a corporate body, has a right to choose what they want to air. First they chose to air Duck Dynasty, then they chose to suspend Phil Robertson. Both choices are entirely within their rights, regardless of their reasons for doing so. Also, suspending him is not an attack on his freedom of speech.
To use an analogy, if I give you a megaphone with my name on it and you say something I don't like, I have every right to take back my megaphone. Your right to free speech is completely separate from the privilege of using my megaphone. His right to free speech is not tied to the privilege of using A&E's platform.
Some Christians argue that suspending him from the show for articulating his beliefs is an attack on Christianity. Some gays argue that the passage he paraphrased is an attack on them. Both sides have the right to state their beliefs. Freedom of speech is not freedom from consequence.