I don't think it's a money issue as much as how the money is being collected and what it's going toward.
If you told a new player the money was going toward the IFPA to provide services to maintain a website and organize tournaments and to promote pinball I think most people would be on board.
If you tell a new player this money is going to a fund the prize pool of elite players and you have little chance of seeing it unless you play very well and enter every possible tournament you can to earn all the points you can I think most people would scoff at that.
Charge a yearly administrative fee of $5 paid through the IFPA website. If you pay you get ranked in all the tournaments you play on for the year. If you don't pay your points will count as if you played in the tournament so other players don't get screwed over but you cannot see your points on the website.
Calling it a fee also hopefully gets around states with gambling laws like Wisconsin.
If the IFPA wants to use 100% of your $5 for prize money that's fine. They can do what they want with their "fees."
Do not do this amateur vs. pro separate tracking. Keep it simple!
The collecting $1 per tournament from players 1/2 of which are willing to pay and the other 1/2 are not then sending the money to IFPA, designated who did and didn't pay for that particular tournament is a logistical disaster.