If you haven't seen this ad yet, watch it now so you have some idea what I'm talking about:
So on to the more pertinent question: what exactly is wrong with what he said? Imagine if he had instead said any of the following were heinous:
"...that Christians can serve openly in the military, but gay teens have to worry about bullying in schools." Media darling.
"...that gays can serve openly in the military, but Muslims have to worry about discrimination." Again, mad media props would be forthcoming.
"I'm gay, but I think it's absurd that we have convinced the military to let us serve openly while Christian kids have to worry about not being allowed to pray." The mainstream media – I guess – would be dumbfounded. Sort of like they ignore the Log Cabin and other homosexual (or women's) conservative groups. (Note: I am not suggesting that Perry is a homosexual, if for no other reason than I try not to offend people. This is a purely hypothetical scenario. Why do I feel like this CYA disclaimer is necessary?)
And on the facts of what Perry said, it's really not that outrageous. Recently courts (and the threat of the courts) have been limiting, or trying to limit, not just "official" school prayers, but prayers by anyone associated with a school – even student groups.
As for what he said about the importance of faith (especially Christian faith), we may have "moved past it" in much of the public mind but he's following a long American tradition, going back to Lincoln... the Founders... the colonists... the point is, are we now going to discriminate against a man on the basis of finding his religious faith uncomfortably real? What's the real difference between that and discrimination against someone because we find ourselves uncomfortable around a flaming gay?
Right... religion. Christianity is one; being gay isn't. Which brings me to a constitutional point. The relevant text would obviously be the First Amendment:
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.
I can see several possible interpretations of this:
Historically speaking, it recognized that religion (meaning as such the various Christian sects, though the extension to other religions follows logically) is a unique category of behavior, and speech; and that given religions exist, we treat the nature of the subject with respect, but studiously avoid all legal favoring of any one religion. (Incidentally, this renders the National Cathedral an extremely curious artifact, let alone trying to figure out which clergyperson should be allowed to officiate there. Why do we have the thing, anyway? Not that it's not impressive.)
A more modern interpretation suggests that religion is to be removed from the "public sphere" entirely. Driving this are various ideas, from explicitly anti-religious sociology to a reasonable reticence in offending others to a growing casual unbelief.
However, on strict textual grounds, it would seem (and this is the third option, which is both straightforward and tolerant) that while religion is explicitly barred from receiving favored treatment, all speech is still protected – and this includes religious speech. Which brings me back to the point I think Perry was trying to make. We preach tolerance, especially for historically persecuted groups... but still prove intolerant of other groups. The fact that they've been historically favored (in this country) doesn't excuse this behavior.
A secular country – assuming that's what the USA is, and we can make a plausible argument this is true at least in modernity – has to, almost by definition, regard religious speech as just another kind of speech. To do otherwise is to either legitimize the supernatural in public affairs, or to declare itself not secular (which is to say, sticking to common things) but expressly anti-religious.
Anti-religious? Not a reasonable option. I would feel extremely confident in arguing that in the state of Alabama – to pick on the "Bible Belt" – far more death threats are issued each year over the Iron Bowl than over matters of faith or any discrimination "ism". Obviously we need to ban football from schools. Or maybe just 'Bama fans, I'm not sure. After all, we're kicking Christian prayers out while championing idiots suing Catholic universities for not being Muslim...