You are painting with a mighty broad brush here. Is it really fair to lump all churches together with this statement? Money itself isn't the problem, it is the love of money. The complete quotation which you cited in your question is:
For the love of money is a root of all kinds of evil. Some people, eager for money, have wandered from the faith and pierced themselves with many griefs. - 1 Tim 6:10
The verse itself answers your question. People that pursue money rather than God have wandered from the faith. Churches are made up of people and all people are susceptible to the allure of money or any other vice for that matter.
People of faith, any faith, are just held to a higher standard because they subject themselves to that standard by their profession of faith. People don't look down as much on an atheist who wantonly pursues money because they don't profess to be above it but is it really any better? Just my 2 cents...