I think this might be about a power struggle between the pro-academic programs parents and the football booster club parents. In New Jersey, there is, in some districts, a bitter battle between the two groups over funding. The football parents are often well organized and succeed in getting funding (for fields, etc.) and the parents of non athletes resent it. They might be bent out of shape that some academic program with little student participation like for example, the Russian language department, lost funding. Often the non-athlete parents are supported by the local teachers union. The teachers' union wants to preserve academic programs to keep staffing levels as high as possible. The battle between the two groups over funds can be very vicious and get personal.
This complaint about prayer might be an act of retailiation against the football program by parents holding a grudge against the sports program, or against the coach and players' parents.