From just a quick read-through, here is what I think is the core holding:
While it is possible to conceive of fees that are impermissible because they are so exorbitant as to deter the exercise of the protected activity, see 729, Inc. v. Kenton Cnty. Fiscal Court, 515 F.3d 485, 503 (6th Cir. 2008) (concluding that the Supreme Court’s fee cases “created some limit on the amount the government could charge, based on the potential for a fee to deter protected speech”), there is no showing that the $340 handgun licensing fee qualifies as such a fee. The plaintiffs merely assert that the $340 fee is excessive, which is not sufficient to raise a genuine issue of material fact regarding the permissibility of the fee. See 729, Inc. v. Kenton Cnty. Fiscal Court, 402 F. App’x 131, 133 (6th Cir. 2010) (“Merely asserting that the fee is exorbitant, without evidentiary support, is insufficient to withstand the County’s motion for summary judgment.”). There is no evidence that the fee has deterred or is likely to deter any individual from exercising his or her Second Amendment rights; indeed, all of the plaintiffs have paid the fee and have not pointed to any particular hardship they faced in doing so.
Opinion at pp. 21-22.
The opinion then goes onto discuss some legislative history indicating the cost of administering the the program was as much as or more than the $340 fee.
The fact that the money goes into the general fund, rather than earmarked for a special account, is of little relevance. Most government programs are paid through the general revenue funds; e.g., prison operating costs. The bottom line is that the plaintiffs were unable to offer any proof that the $340 fee substantially burdened their rights.
Perhaps a better factual scenario may have made the difference; a poverty stricken war hero threatened by hooligans and unable to pay the $340 fee. We should remember the maxim, "Bad facts make bad laws."