Last night I got a letter from Shippensburg University that stated they would no longer being accepting Visa cards for online payment of classes. The reason Visa has dropped is because the university is looking to begin charging a "convenience fee" for using credit cards which will theoreteically save the university \$280,000/yr.
The payment processor Shippensburg University has chosen, Official Payments, clearly supports Visa. It is solely the desire to charge this convenience fee that has driven the university to drop Visa as a supported payment method.
It appears that Shippensburg University isn't the only one that is going this route; Brooklyn College has an almost identical story from last september.
I don't think the university has fully through through the cost savings brough to them by using credit cards. They will incur a significant cost if they choose to only accept paper (check) transactions from students. They will incur an even greater cost if students decide to stop taking classes from this decision.
Personally, paying by Visa was my only way of meeting their ridiculously short deadline for payment (typically two weeks from the time you get the bill), so it's likely I won't be continuing my graduate studies at Shippensburg University unless they reverse this decision.