I agree. Without an efficient micropayment system available, I can understand a charge per transaction. But adding a transaction fee to each pledge, when the patron is making one monthly payment, is a bad idea. Maybe they want to get rid of patrons supporting lots of people at low levels for some reason.
They could argue they're potentially paying a transaction fee when they're paying the creator if you're the only patreon. That's a silly argument though. I'd be happy to pay a single 2.9% of my total pledges + a single 35c fee.
This just kills $1 donations (and in my mind: anything up to $10)
It seems that they might also be de-aggregating pledges - which means not only will you be paying the 2.9% + 35c on each pledge, you'll also get N charges on your card rather than one. There was also some other hint that pledges would continue to be charged on the day you signed up rather than the 1st - just to make a triple whammy of idiocy.