The one direct subsidy to religions in the United States every year is the money given to religions through the White House Office of Faith-Based and Community Initiatives. In 2009, that amount was $2.2 billion, though additional money can be given to religions at the state level.
MORE: http://c3414097.r97.cf0.rackcdn.com/120516SecularHumanism.pdf
See also...
Should Religious Organizations Benefit from Tax Breaks?
http://www.americanhumanist.org/HNN/details/2012-05-should-religious-organizations-benefit-from-tax-brea