They do, to an extent. In the first season, on at least one occaision during one field mission Ford switched to US-standard digital camo fatigues. Here's a quick rundown of the USUAL uniform assignments:
Season One:
-Civilians wear beige uniforms, with blue panels (science), green panels (engineering/technician) or yellow panels (medical)
-Military wear light grey uniforms, and black panels
-Civilian leaders wear light grey uniforms with red panels (Weir, Teyla)
-Weir got a thinner, more form-fitting grey jacket halfway through the season
Season Two:
-The military guys got darker grey uniforms. Select nonmilitary guys got them too (McKay, Beckett, Zelenka, etc.) though they didn't always wear the coloured panels with them.
-Weir got sick of her jacket in this season and started wearing off-the-shelf tops and jackets from Lulu Lemon. :P She would still wear her old jacket for official stuff and field duty.
Season Three:
-Sheppard got a cool aviator jacket, and eventually phased out his gray uniform in favor of the standard black BDUs that the people at the SGC wore. He's the ONLY military guy to do so; everyone else on Atlantis continued with the grey/dark grey uniforms, notably Major Lorne.
-McKay likewise phased out his uniform for the usual blue BDUs seen on SG-1. Rumour has it that the actors hated the outfits and in the abscence of new ones, just started raiding the SG-1 warddrobe as that show was wrapping up.
Season Four:
-McKay, Teyla, Keller, Carter and Zelenka get cool new outfits with the panels replaced by striping.
-Sheppard maintains his black BDUs. All other militaries stay the same.
-The field uniforms for Sheppard, Teyla and McKay are replaced by black field uniforms pretty much like the ones used in SG-1
Season Five:
-Woolsey wears a new-style uniform, but in a lighter shade of grey than everyone else
-McKay and Teyla start wearing the same cool leather jackets occasionally in the field, most notably during the episodes films in the colder and wetter Vancouver winter.
Whew!
Mark