I've talked religion with people of many different ages and creeds, and none of them have ever been content to practice their religion in private. All belong to a religious community; many contribute money and time above and beyond the minimum requirement. And in all the religious discussions I've ever had, I've never heard anyone decline to participate because their religion is "intensely private and individual."
So Eliezer's quote from William James by way of Adam Frank left me scratching my head, as well. I think of religion first and foremost as a social behavior rather than an individual one. It's not just that religious people use the claim of private revelation as a defense against reason; it's that they can attend sermons, sing in a choir, recite prayers in unison--and then make that claim of "solitary" experience with a straight face!
Eliezer's post listed some of the ways that theodicy warps rational thought on the individual level, as sort of warning label on the "poisoned chalice." Religious people are liable to respond that religion may not make people rational, but it makes them altruistic "good Samaritans." (Never mind that in the parable, the Samaritan is more altruistic than a high priest!) They claim that any harm religion does to the individual is outweighed by its benefits to the group.
Rationalists should make the case that religion is harmful to society as a whole, as well as individuals:
- Religious groups waste resources. I couldn't find exact figures, but Austin Cline claims that tax-exempt religious organizations own 20-25% of land in the US, denying the government billions in tax revenue. Donations and tithes to churches are wasted on funding monasteries, missionaries, and "bible schools." Rationality dojos, or even the government, could allocate these resources more effectively.
- Religion degrades political discourse. Clergymen have an inappropriate amount of involvement and influence in the politics of their congregations, e.g. Catholic bishops denying communion to politicians who support abortion rights. The Terry Schiavo debacle demonstrated that American right-wing religious groups are willing to use political power in unethical ways. It's a national disgrace that no non-Christian could be elected President in the US today. (I don't mean to be US-centric, it's just where my knowledge is concentrated. If you have an example from another country, please add it in comments.)
- Organized religion obstructs social progress. Because religions are based on dogma, they have a status-quo bias that has placed religious institutions on the wrong side of every moral issue in American history, from the abolition of slavery to Prohibition to stem cell research.
- Religious pluralism and state-sponsored religions both harm society. Many competing religions contribute to social fragmentation and create useless discord (as opposed to the useful discord of, say, a free market). A single state-sponsored religion inevitably intrudes into citizens' privacy and the political process. The optimal solution is an atheist society.
I left out at least one obvious argument for the benefit of commenters.