Simple, it was not designed to put up with entering atmospheres because it was not necessary.
To expound further: ships like the USS Voyager in the 24th century were designed to enter a planetary atmosphere and land, and therefore would have been designed with hull plating that could withstand the thermal stress of entering a typical atmosphere (assuming a reasonable angle of entry). Shuttlecrafts are in a similar boat. None of the Enterprises that we've seen, however, were designed to land under normal circumstances, so while their shields could probably take the heat, an unshielded atmospheric entry would be quite a problem (as we've seen on a few occasions).
It can, although in normal operation, it doesn't. The NX-01 Enterprise is seen to enter the Earth's atmosphere in the ST:ENT episode "Storm Front". Also, the Enterprise, NCC-1701, is seen in the Earth's atmosphere in the ST:TOS episode "Tomorrow is Yesterday". The Enterprise-D enters another planet's atmosphere on at least three occasions: during the ST:TNG episode "Arsenal of Freedom"; during the "award-winning" ST:TNG episode "Deja Q"; and, during Star Trek Generations. Certainly, even without deflector shields or hull plating, the hulls would be able to withstand the frictional heat of atmospheric entry. ProfessorTrek 02:58, July 1, 2011 (UTC)
Hull temperature is not a problem. Shields exist for that and we've seen on multiple occasions even an unshielded shuttle survived a high speed descent and of course a high speed descent is not the only way to enter an atmosphere. The real problem is the power of the thrusters and structural integrity (though that last one only comes into play at high speeds or a landing). The Enterprise can enter an atmosphere as long as it doesn't go too fast, it cannot land however.
126.96.36.199 22:01, January 30, 2012 (UTC)