The front element of a lens is still (and probably always will be) a lens element, usually the largest and most expensive single piece of glass in the system. If you need physical protection for that element, you still have to add it (where the lens design permits).

Every element in a lens system contributes its own refraction and reflection. When you put an extra element at the front of a lens, light that would have reflected from the "old front" harmlessly into space will now reflect off of the rear (and front) surfaces of the new element. Those reflections can be minimized with coatings, but they are still there, and they still contribute to a degradation of the image. And keep in mind that the new element, whatever its shape, will still refract light and add its own distortions.

So you have a choice -- use the lens naked for best optical performance, or add a filter. When the filter is used for photographic reasons (neutral density, polarizers, color filters) you have a trade-off that's worth the price -- you give up the ultimate performance possibilities of the lens in order to capture a picture that the lens alone could not have captured.

You may be of the opinion that protection of the front element is also a reasonable trade-off at all times. I'd only use a "protective" filter if I was working in an environment that's likely to cause damage (say a windy day on the sand dunes or photographing someone using a grinder). For knocks and bumps, a lens hood offers good physical protection without putting anything in the optical path. But it's your choice—and it should remain your choice.