A lot of the E-ZPass system is about the simplification of the back-office processing. When you get a transponder, you have an account set up to do the debiting and also identify your current mailing address. License plate recognition, by contrast, requires getting details from different databases, and the mapping to the vehicle owner is less robust. It really is easier for the toll providers if they use a transponder system than it is to do license plate recognition.
Also, E-ZPass is an interagency consortium, not a company. It's actually largely run by the Port Authority of NY and NJ. The only fee that appears to be collected is a one-time $10 to use the trademark.