Vandalism has been an ongoing topic in the freethought community since we "new" (or "Gnu") atheists started advertising our presence via billboards and banners on city buses. Even ads that make no attempt to demean anyone's beliefs and simply state facts like "Millions are good without God" have been vandalized. I don't know whether the vandals consider themselves Christians, but if they do, I'd actually be pleased on some level. On the other hand, I take no pleasure in the news that two Christian churches in Bend, Oregon were vandalized by someone who sprayed "Flying Spaghetti Monster" slogans and graphics on their buildings. The vandals have been caught, and seem to regard their work as a "near-harmless" prank for which they've paid by cleaning up other taggers' graffiti. They've rationalized their actions by saying that they used washable paint and just wanted to "make a point" and bring some "fun" to the city. Does that mean it's OK for someone to spray-paint a smiley face on my house using washable paint, because it's easy to clean off and might bring "some joy and fun" to my neighborhood?
Hemant Mehta at FriendlyAtheist.com rightfully deplored the defacing of the buildings and requested donations to help the churches clean up the graffiti. A couple hundred of his readers responded and raised nearly $3,000. That doesn't surprise me at all. What does surprise me is the number of people who commented on his blog and elsewhere that they just couldn't donate money that would be used to support a church (to which Hemant replied, "You’d be giving money toward the clean-up costs and nothing more"). In the end, both churches whose buildings were defaced cleaned up the graffiti themselves and declined the money, so Hemant forwarded it to the Foundation Beyond Belief.†
If a church (or synagogue, or mosque, or Scientology center††) was damaged by a natural event such as severe weather (an "act of God"!), I wouldn't donate money or time to repair it, nor would I urge other freethinkers to do so (although I wouldn't criticize those who wanted to help). I wouldn't urge atheists to help clean up graffiti at Christian churches if they felt that wasn't the best use of their time or money; I don't think that we're all obligated to atone for the actions of a few freethinkers.††† But in the face of criminal acts, isn't declining to help the vandalized churches solely because they are churches kind of like Christians who act honorably...but only toward other Christians?
† Foundation Beyond Belief is "a 501(c)(3) charitable foundation created to focus, encourage and demonstrate the generosity and compassion of atheists and humanists." I'm a contributing member and recommend it highly.
†† A Scientology center in Ocala, Florida that prominent Scientologist John Travolta helped open a few weeks ago had the letters "ANON" spray-painted on its windows, presumably as a reference to the group "Anonymous" that has targeted the Church of Scientology.
††† Or at least those who commit mayhem using phrases and symbols associated with freethought. I don't know whether the vandals consider themselves freethinkers or not.