I think the main problem occurs when you have to split player character resources between space combat abilities and regular combat abilities (and possibly other abilities not related to combat). You have the Top Ace Pilot that flies the ship and fires the guns and all that, and the melee guy that ... hates space combat because he can't swing his plasma sword at anyone.
Ah but that's why Melee Guy needs to either have a starfighter of his own or some other skill that helps in space combat.
In my Star Wars (D6) campaigns is was common for the Merc/Soldier types to have a higher Starship Gunnery then the Smuggler who Pilots the ship. The Smuggler gets to do all kinds of fancy flying while the fighter type fights by shooting the guns. Co-pilot switches between Shields, Sensors (got to find the enemy's weak spot) and repairing damage from shots that did get through.
Actually for me this is RPG Space Combat 101 since I've spent so many years gaming Star Trek and Star Wars. Traveller can work this way as well.
Thing is, if everyone in the group is a ground pounding future soldier space combat will indeed be boring. I would have it occur rarely and become more of a background atmosphere element. The trick to good SF gaming is that vary same thing that Fantasy tells you not to do...split the party. If you can develop good timing and staging skills as a GM the players in a SF campaign are in for a real treat. The melee characters can be duking it out in the corridors with boarding pirates or down on the surface of a world while the ship's crew battle swarms of starfighters and try to repair the hyperwarp drive at the same time.