Some churches are far from non-profit. How else could they expand so rapidly, with churches all over the country? Also, either all churches are taxed the same amount, or they're not taxed at all. That's the only way to make sure the government isn't favoring a certain religion or church.
Not taxing the churches works better. Why? Because by making the churches apply to be tax exempt, you don't have to deal with the subjective problem of the government deciding what should/shouldn't be taxed, because there are hundreds of variations of churches.
Religious organizations shouldn't be tax exempt because they are religious; they're not needed for someone to practice their belief. However, if they are non profit, they should be entitled to all of the benefits that any other non profit organization does.