You generally never want to take A/E/J/Z because they're sooo much slower than LIRR, unless you live along them.
Yes, LGA is far worse.
Bart from SFO to downtown SF is about $11 due to a surcharge and the combined fare AirTrain + subway is also about $11.50. LIRR is a bit more expensive. The Paris RER is €13. I don’t see how the fare is objectionable.
I personally appreciate the subway connections exist. Taking LIRR would require a subway transfer to most destinations anyway.
And like I said, you don't want to take the subway unless you live along its route, it's so much slower.
If you need to pay for the construction cost of the AirTrain, it should just be funded as part of the airport generally, because that's what it is. Charging for it is as silly as if you charged to take the AirTrain between terminals.