Numerous ways as the 2 PP's have said. The rental agencies also have a couple different way they will go about charging you as well if you don't have a transponder.
1. If you don't go through a toll nothing happens
2. If you go through a toll they charge you a fee per day for ever day you had the car plus the toll.
Avis charges 3.95 per day even for days you didn't go through a toll. They bill you later on your credit card
3. Charge you a fee only for days you go through a toll plus the toll. I believe
Alamo does this, it's 3.95 any day you use a toll plus the toll. Again you get billed later.
Best bet is to look at the website of the the car agency you will be using or google it to find out how the charge. I'm not sure how it works if you wanted to "Pay By Plate" so be sure to read through their websites for info.