Running a charity does not mean people should not be paid appropriately for the good work they do. And FYI, “appropriately” means as much money as allows them to run a financially sustainable program. If you’re paying yourself even $250k a year but keeping some children fit, opening college doors for them, and the non-profit isn’t losing money, by all means take it. If Joel Osteen can take home $50 million plus perks in his career while locking the doors to keep out the homeless and needy, certainly a guy running a youth soccer program who actually helps kids should be able to make 0.5% of that per year.....
If the league or the member clubs are 501c3, then they claim to be running a charity to promote the game. That is different from claiming to run a private business.
Regardless, “appropriately” does not mean what an anonymous internet poster who has never run a real business thinks is too much or unfair. Your belief that a non-profit soccer club’s goal should be “to promote the game” is just wrong. It is to try to provide whatever benefit the non-profit chooses, which comes in many different forms. Maybe exercise is enough for many kids. Maybe opening college doors. Maybe keeping kids out of trouble.