They do indeed offload the same way as other APCs once they're on the ground. Larger aeros such as Small Craft or DropShips are a bit different, but that's outside the scope of this discussion.
The risks of takeoff and landing, lawn-dart rolls, lack of cover, lack of TMMx the fact that a lot of folks don't understand aero rules and/or view them as a hassle...there's a lot of reasons why someone might prefer VTOLs over aeros for their soccer mom transport needs.
On the other hand, aeros do have advantages. It's safe to assume that your typical aero will NOT have a hit location with only two armor on it. Most troop-carrying fighters are far more heavily armed than any transport VTOL, giving your infantry contingent organic fire support. (For laughs, try keeping the fighters on the ground and using them as rolling assault guns that don't suffer vehicle motive crits.) Aeros have more offloading options than VTOLs, able to land and unload normally, drop jump troops from very low altitude using the rules in TW(think of the "Downloading" maneuver from Wolves on the Border), or drop troops from higher altitudes using the Dropping Troops rules in SO.
As for how many factions actually think this is a good idea...it should be pointed out that while uncommon, there are still multiple troop-carrying fighter configurations or variants out there, from the ubiquitous Planetlifter, Kirghiz and Troika variants, and the purpose-designed Yun, plus any others I've forgotten.