I'm also completely flummoxed by the people saying a consecrated host is JUST A CRACKER, so why is everyone getting all upset?
Would it be okay if I spraypainted obscenities on your mother's grave because it's just a piece of highly compressed igneous rock with some lines chiseled into it? How about if I photoshop your a photo of your now-grown child onto a piece of child porn, because after all, no one's actually hurt by this--it's just a piece of paper.
If you reduce symbols to their base physical constituents, then of course it sounds silly to get all excited about them. Nonetheless, you'd probably be pretty damn upset if someone dug up a relative's grave and desecrated the corpse on the grounds that it's just some rotting meat.
People do not live without symbols. The fact that you do not share someone else's symbols does not give you the right to descrate them. Desecrating other people's symbols is the act of a bully and a boor.
Atheists have done better out of America's committment to pluralism than any other religious group, so it's hard to see why any of them would now condone an attempt to break down the social compact that demands that we mostly leave other peoples' religious beliefs alone. Yes, yes, I know--evolution!. Except, ummm, the Catholic Church isn't against evolution, and most of their energy is devoted to perfectly acceptable civil practices like boycotting sexy movies and complaining that everyone is mean to them. When you catch Bill Donohue pissing on PZ Myers' grave, come back and we'll talk.