Military planes - Super Hornet, for example - have been using touch screens (UFC, in this case, the thing just below HUD) for over two decades now, and they seem fine with it, and newer ones use it even more. They don't seem to cause any problems.

Granted, stuff that's absolutely critical - like gear or the arm switch - is still mechanical, but UFC is still pretty mission critical, controlling eg IFF, autopilot, or radios.