I'm not sure if I *checked in* online, but I used online payment to avoid the counter on my last trip in April. My card was not charged until after I dropped the car off.
I just rented a car through Alamo 3 weeks ago. I used online check in. It was a breeze! Go straight past that loooong line to parking garage and get your car and drive to exit with your paper work. Your CC is not charged till after you return your car.