1 Timothy 6:10
King James Version
10 For the LOVE of money is the root of all evil: which while some coveted after, they have erred from the faith, and pierced themselves through with many sorrows.
It is the love of said money, rather than the money itself which is the root of all evil, as it is this lusting after currency which drives the evil. But to answer the question, in regular sized churches where they pass the offering plate the money usually goes to pay the bills such as water, electricity, mortgage or rent etc... some usually goes to charitable needs, I assume the pastor and other clergy folk get paid a salary as well. However the likes of the megachurch variety where a lot of money is pulled in who knows. I would file that one under the LOVE of money and I assure you, God is not in such a church.