Yeah I work for the state. They recommend everyone use direct deposit for a lot of reasons, but we have not only our own internal payroll system but an internal auditing system.
So go figure.
But yeah, payroll companies only charge more for direct deposit because it's a "bonus" feature. It's smart because it usually costs the payroll company less over time. According to my friend, a CPA, there's an initial charge to get everything set up with the bank as well as a basic cost for each paycheck but overall after all the costs add up his company found it to be about 73% cheaper to just do direct deposit, and the companies usually preferred it because float is nice but there are penalties to late deposits that the company could be held liable for, so they prefer to do it directly.