Freedom FROM religion does not inhibit freedom OF religion.
Take the pledge of allegiance for example: it contains the words "under God". This forces every American citizen who wishes to pledge allegiance to their country to make a religious statement of belief in God, even if they are atheist. In this case, they do not have freedom from religion, as religion is being forced upon them.
Taking these words out of the Pledge of Allegiance in no way infringes upon the freedom of religion of Christians. They are still free to practice their religion, sing psalms at church and praise the lord 24 hours a day if they want. All they have lost is the power to force everyone else to make a statement supporting God (and since the US is predominantly Christian, by extension supporting Christianity).
A compromise? Simply have two varieties of the Pledge of Allegiance. One for citizens who wish to make a religious statement in their pledge, and one for those who don't.
It is worth remembering that all those people burnt at the stake during religious conflicts in Europe were not killed because they were practising religion, but because they were not practising a particular religion. They did not have the freedom not to be of a particular religion. It is unfortunate that, while Western society has progressed to the point of allowing people not to be of a certain religion, there is still some way to go before people have the freedom not to practise religion at all.