My point of comparison for atheist orgs are national LGBT orgs, which always receive a healthy amount of criticism from the people they are supposed to represent. In my view, atheists do not criticize atheist orgs nearly enough, and it's as if most atheists don't even know how. Here I present a few general lessons I learned from the way queer people criticize LGBT orgs.
1. Losing in court may be worse than nothing. When DOMA and Prop 8 were brought to the US Supreme Court, many activists were worried. Is the Supreme Court ready for this? If the Supreme court rules for DOMA and prop 8, it would set a bad precedent that could stick around for a long time. These fears did not play out (SCOTUS ruled against DOMA, and punted on prop 8), but they were reasonable fears to have. Regardless of the merits of AA's case, we should be seriously asking whether they are likely to win or lose.
There is something to be said about bringing something to the table repeatedly to keep it in the public consciousness. For example, LGBT orgs are constantly bringing up ENDA to the legislature even though they know it will lose for a long time. However, the argument here is that ENDA is good PR even when it loses. Whereas it is obvious to anyone that AA's case against the WTC cross is very bad PR. I cite the comedians.
2. Priorities matter. Here on the internet, it is poor taste to compare the direness of two issues. When you say "there are starving children in Africa" or "Women in the middle east have it far worse", that's really just a way of shutting people up. The thing is, it doesn't cost anything on the internet to talk about all issues, big and small. But when it comes to national orgs, they have a limited budget and it costs lots of money to do anything. Abandon your preconceptions about "oppression olympics"--they do not apply here.
Mind you, smaller problems often cost fewer resources, so this doesn't mean orgs should always just focus on the biggest problems. However, I suspect bringing a court case to the 2nd Circuit of Appeals is not that cheap? One of these days I'm going to look into atheist org budgets to see if I'm correct.
3. Priorities are set by the privileged. One of the major complaints about LGBT orgs such as the HRC is that they focus too much on marriage equality. This is seen as disproportionately representing the needs of people who are well-off--the people who donate most to LGBT orgs. I suspect that younger critics aren't very familiar with the many ways that marriage equality is substantially beneficial to immigrants and people of lower socioeconomic class, but I see their point. People aren't going to get married if they're bullied into suicide, or if their society prevents them from finding partners, you know?
I wonder, who funds American Atheists? Probably a bunch of older people who are financially privileged. It's only natural. Are these people sufficiently educated about the problems of the common atheist that they can set their priorities right? Do they have our best interests at heart, or their own best interests at heart? It's like that time that Michael Newdow filed a lawsuit to remove "God" from US currency, he cited testimony from old numismatists. That seems like a horribly nonrepresentative group of atheists, doesn't it?
You all deserve better atheist orgs. Criticize the ones we have now.