Rob Mitchell has noted to me that those of us who object to the phrase "In God We Trust" on US paper money have an easy form of protest available to us.
Simply black out the offensive words with a felt tip pen. You'll be taking direct action to make the currency better, and every bill you alter and spend will circulate your opinion of 31 USC 5114(b) far and wide.
This idea seems to have been re-invented several times. Google finds a number of web sites advocating it, such as this one, for example.
I'm sure I'll get mail claiming that marking your bills in this manner is a crime of some sort, but it appears that, arguably, given the intent and result of the action, it is does not meet the definition of defacing the currency in the U.S. code. Apparently adding an advertisement to the currency is illegal, so I would stick to merely inking out the offending phrase rather than adding any words of one's own, even though the statute seems to be discussing commercial advertising. Also, merely inking out the phrase makes it less likely the bill could be argued to be "unfit to be reissued" given that banks put ink marks on bills all the time.
(Rob argues that just inking out the offending phrase is a more powerful statement anyway, and I tend to agree with him.)
Regardless, the activity is probably protected by the first amendment, and as a practical matter, the odds of anything happening to you are likely nil.