The short answer is freedom of:
"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."
Lots of commas and semi-colons.
The first clause. "...make no law respecting AN establishment of religion, or prohibiting the free exercise THEREOF;" (emphasis mine)
The highlighted "thereof" is where most people point and say "See, freedom of religion" and libs say "See, freedom FROM religion". I blogged about this before, complete with Websters and Oxfords definition of "thereof". I don't feel like repeating myself, so go dig through my archives. The upshot? The founding fathers meant, and they expounded on this in the Federalists Papers among other places, you're free to practice, don't practice, whatever, pray, don't pray, God, Ghu, Nature, Glaciers (The Great Pumpkin help us), Trees... well you get my drift. If you want to dance naked around trees on the summer solstice and that's how you worship whatever you worship that was honky-dory with our founding fathers.
The "an" on the other hand. You see, the libs, and this is just my guess, look at "establishment" as a verb. The "an" on the other hand sort of forces "establishment" to be a noun. And therein lies the rub. The libs read that and say "Look! Separation of church and state! See, you stupid conservative bible banging idiots.", and then laugh in a condescending and superior way.
Which is ironic.
Because the "an" is sitting there right in front of "establishment". The noun establishment is a different beast and sort of makes the libs wrong. Which means they're... well, the idiots in this case and even dumber for laughing at the conservatives about it.
At the time the First Amendment was drafted, most, if not all, of the 13 states had official state religions. So, the founding fathers were limiting the federal government from stepping on what they saw as the purview of the states. Which is what the first 10 amendments are all about. Limiting the power of the federal government.
So, "establishment of religion" was meant to be a fancy way of saying churches. Or any organized religious body. (The sticky bit here is that read that way, it makes all those laws exempting churches from taxes unconstitutional)
On a side note, the complaint is if churches had to pay taxes they'd be paying things that were against their beliefs, like abortions and civil union marriages, etc. I'd counter with two arguments. Show me where in the constitution abortions are enumerated. Or for that matter where does it say ANYWHERE that the government has any business in marriages?
Secondly, the government has it's fingers in places that would make the founding fathers flip their powdered wigs. Things like soup kitchens, housing the indigent, orphanages, etc were originally funded in a secular manner by the churches and local charity organizations. If they were put back in their hands the churches wouldn't have to pay taxes for things that were against their beliefs. And besides, I have to pay taxes that go for A LOT of thing I don't want to pay for, why should they be any different.
But I digress.
So, when you look at the word establishment as a noun, you sort of make the concept of separation of church and state vanish from the first amendment. But as it was never there in the first place, that's not that amazing.
People have an astonishing penchant for reading the constitution using modern definitions. Which is boggling when you consider that the people writing the stupid thing could have no way of knowing how the definitions would evolve. They wrote using words with definitions that were valid for their time. We should read the constitution using those definitions, NOT ours.