To date, there hasn't been a single episode or movie to suggest that starships couldn't cope with atmospheres or landings. Indeed, "Arsenal of Freedom" shows the E-D entering an atmosphere and then going through the extra effort of making it dangerous to the ship, so that a shadowing enemy ship would also be put to jeopardy.
And previous Trek precedent: the still heavily damaged NX-01 making a strafing run on Nazi-occupied New York in "Stormfront Pt-II." In the 24th century, we see USS Voyager making a controlled landing on a planet on three separate occasions, and years later doing a low-altitude flyby of the Golden Gate Bridge to celebrate its homecoming. There's also USS Defiant jousting with Jem'hadar battle bugs in the atmosphere of a gas giant in Starship down; atmosphere and gravity conditions at least 100 times greater than any terrestrial planet.
Seems even relatively primitive starships can handle atmospheric flight easily enough.