I think the idea of unit movement and turn durations can be reconciled with the following interpretation:
Moving a unit from one tile to another represents more than just sending some troops out on a foray. It represents establishing a "base" for that unit from which it can exert influence and control over the local area (ie that tile directly, and bordering tiles indirectly with the ZOC ability.) If units from 2 different civs attempt to control (ie "move into") the same tile then there are a series of engagements which will eventually cause one unit to surrender/die, or in some cases retreat.
So, in the first turns of the game, moving a warrior from one tile to the next taks 50 years because what it means is that your civ supports a warrior "caste" or tradition in that tile. Moving that warrior means reorganizing the whole society that supports that unit (whose members span a couple of generations) so it can exert its control elsewhere.
As the game progresses, the turn time decreases, representing the increasing control of governments over people. But moving a unit still means moving all the bases, the soldiers' homes, or the supply lines to those homes, and maintaining transportation between the tile the unit occupies and the home country. During the span of a turn the individuals in a unit may travel back and forth many times, but "moving" the unit, ie reoganizing the base of operations and thus the influence that unit can exert, takes time.
Until the industrial revolution, that is, and the development of rails. Sure, tanks could drive across the country, given a year, without rails, but how the heck do you move the heavy equipment (garages, lifts, parts factories) and relocate the personnel that support the tank unit without heavy transportation capacity? Basically, spend a year taking it apart to ship to the new location, or rebuild some of it at the new location.
I know there's problems with this interpretation (ship movement takes a bigger stretch of the imagination), but it does rationalize why rails can provide free movement within borders while roads can't. Though I agree with some posters that modern superhighways fulfill the same role as rails, this does not necessarily coincide with the "roads" that the workers build.
In any case, I don't have a problm with the way rails work WRT movement or production/food bonuses. I think it's wise to assume that in the late game the "rails" also include superhighways, though remember rails still exceed roads in terms of gross weight capacity. You eventually need highways just to take some of the lighter traffic away.
Finally, this gives a reason to allow rail movement while restricting airlifts. Making units wait a turn after airlifting demonstrates the logistical difficulty in getting not just the tanks/trucks the unit needs to the new airport, but also the fuelling stations and maintenance garages.
Hope this makes sense, and note this is just a suggested way of interpreting CIV3 as it currently stands, not an attempt to shut down good ideas for changing it.