I don't mind a modest surcharge for substitutions or special requests. As I see it, the restaurant is telling you that they'll do it if you really want it or need it, but they aren't particularly keen on the practice in general, so they don't want to encourage it. That's better than a strict no substitutions rule, which some places do have.
Because special requests do take more work for the staff, and as katycoo said, it also interrupts the flow in the kitchen.
I'm curious about how the rate of special requests has changed with time. I think there are a lot more special diets these days, for a combination of reasons (fads like low carb, allergies and sensitivities, varying levels of vegetarianism). Special requests are one of those things that tend to be available only if they're not overused - if every customer wants modifications and extras, the management is likely to step in to put some controls on it.