The reason most suits are against small towns, rural counties, and country school systems is because the governing bodies of such areas are almost exclusively the ones who that decide to violate the law. Even small urban areas and bedroom communities know that their populace isn’t religiously homogeneous, so it never occurs to them that they will intentionally engage in unlawful acts just because one of the county commissioners or the president of the school board wants to.

Moreover, if such an entity decides to settle the suit rather than drain its coffers for no reason but to stroke the ego of a powerful citizen, there is generally no opportunity for a court to award a fee, nor has the ACLU lawyer had to invest enough time in the case to justify much in any event; it is very rare for the settlement to include an agreement that the body will pay something for attorney fees, and the lawyers do not have the option to reject a settlement that gives the client what he has asked for just because they would like to get a fee. Even those cases that go to trial almost never result in fee awards that approach the value of the time that the volunteer or staff attorneys have put into it, and in those instances in which the judge has the discretion to deny fees, they often do.

Your idea that no fee is justified since the lawyers are all working pro bono is likewise wrong. Most such suits are handled principally by staff lawyers for the national or state organization (where the state affiliate is lucky enough to be able to afford such a luxury). Staff attorneys’ time costs money, and it is certainly not unreasonable for the organization to recover some portion of the salary they are paid. Moreover, even when attorneys in private practice handle the suit, it is not always pro bono. In the South and plains states, there are generally very few volunteer attorneys who handle all litigation for the state ACLU, and they are most often sole practitioners or with very small firms. In those circumstances, there is often an agreement that most, or even all, of any fee earned will go to the attorney, not the ACLU.

Two final points: you should know that the vast majority of civil rights suits are brought by private attorneys who the objecting citizens hire, and the ACLU and other organizations concerned with church/state problems have no involvement at all (except possibly to file an amicus brief in connection with an appeal from a judgment); the suits of this kind in which it is an ACLU staff or volunteer lawyer representing the plaintiffs only seek injunctions against continuation of the government’s unlawful acts, not money damages. Indeed, one of the criteria for the ACLU accepting representation in any suit is that the plaintiff has been, or almost certainly will be, unable to find a lawyer, because he cannot afford to pay,there is no potential for a contingent fee (because there will not be any money recovery), and the small likelihood of a fee award that will pay the lawyer for his time does not justify him devoting his effort to it, when he has other work for which he is far more likely to get paid a reasonable amount.