Optically-Isolating Limit Switches
Motion control cards generally live in industrial environments, and such things as damage to cables and short circuits are not exactly uncommon. 

Also, immunity to such things as arc welding (Including arc welding where there is a common impedance between the welding supply and the controller), plasma cutting, induction heating and all the other nasty stuff that sometimes happens in a factory. 

When designing such a card, making it usable in the nasty, two systems (one of which is a welding robot) case is a small BOM increase for a lot fewer customer returns. 

Isolated IO is very much a desirable feature in controller cards as it improves the systems immunity to muppet installers and also the immunity to high energy faults.