I pay most of my bills online (amex, visa, ford). And there are no fees associated for any of them. I simply set up the bank account information (account number and routing info) with the respective company and initiate the ACH transfer at my discretion when I'm ready to pay the bill. Been doing it for the last year or so with no problems.
In the long run, it's actually cheaper (although nominally) to pay online since you save the cost of a check, envelope, and stamp. I've saved even more time paying bills by having misc utilities (cable, cell phone, etc) billed monthly to my Amex......then I simply initiate one transfer that effectively pays for ~6 bills. Now, I probably only write three checks a month.....it used to be 12+ every month!