For me, two main things:
1) Reduced WPPR value when a decent amount of people decide they don't want to pay the fee. You know our area, and you know that there are tons of people who don't give a crap about States or rankings, so these people are unlikely to want to pay the extra dollar when they get nothing from it. Too much of that and WPPR values get drastically lowered for the tournament in question. There are people who play purely for WPPRs, as there are those that play for the money (see also: Magfest) and those that just play for fun. NB: I am assuming here that if say, a 50 person tournament only has 10 people who want to pay the fee, then as far as IFPA is concerned it's a 10-person tournament. I'd hate to be someone who planned to travel for a biggie and got 3 points for first.
2) I have personal issues with the potential for people to be opted-in without their consent. Yes, this requires unscrupulous TD's who pay the fee on behalf of others, or who don't disclose that some portion of some funds are being used for this purpose, or any number of other Bad TD Things (tm). It's going to happen though, and since it can be used to boost tournament size as far as IFPA is concerned, this is dangerously close to "paying for WPPRs" in my mind. I've raised this concern before and I know I'm in the minority, so no need to hammer the rusty nail again on this one.
In the end though, this is all just my opinion. I'd be very happy to be proven wrong.