I listed these off my collection ... not exactly prog-rock, because the cookie cutter thing takes away a lot of the far out moments in music ... so hopefully you'll allow me that one moment. Mainly because there were some truly far out things done, that probably deserve a mention!
-- Jon Field -- Jade Warrior
Clay Cook/Jerry Eubanks/David Muse -- The Marshall Tucker Band
Alan Wilson -- Canned Heat
Ray Thomas -- Moody Blues
-- Thijs Van Leer - Focus (and several solo albums!!!)
-- Mel Collins - King Crimson/Camel
-- Ian McDonald -- King Crimson (early)
Ray Herrmann/Larry Klimas -- Chicago
Jerry LaCroix -- Blood, Sweat & Tears (early) and several others
-- Peter Phippen & Ivar Lunde (Experimental Trippy Stuff)
-- Stephan Micus (and other wind instruments) (Experimental Trippy Stuff)
-- Andrew Latimer -- Camel (also the guitarist and main writer)
-- John - Ozric Tentacles (early)
-- Jenny Puertas -- Agusa
Hubert Laws -- Jazz
Paul Horn -- Solo before New Age
Tim Weisberg -- Solo jazz player
Jan Garbarek (mostly saxophone)
Roland Kirk -- Jazz
-- Ian Anderson - Jethro Tull
-- Nik Turner -- Hawkwind
The list would be endless if we used the names and listing of bands that used a flute for 5 seconds, so to speak. I would think that Ian Anderson "owns" this list, but there are some very neat and nice stuff, Jenny Puertas in AGUSA is really good and worth a listen. Jan Garbarek, is mostly saxophone but in his experimental period he also does a large array of flutes with outstanding touch. (Eventyr). Thisj Van Leer had some solo albums way back when of classical music done on flute, and of course he is the great one in Focus. Paul Horn was originally known for his "Inside" series which started with the pyramid and playing his flute, and hearing all the echoes. Nik Turner used the flute many times, but is less known for it, except in some of his solo albums where he shines in the flute, specially the early stuff.
Both Chicago and Blood, Sweat & Tears had flutes at various times, but it is hard to think of them using it as a solo instrument ... I think, in general, the flute was a part of the ensemble ...
Ray Thomas was nice, and I think that the Moody Blues kinda got away from the flute when the band kinda became about the hits and not the music .. .what they started with was gone!
Roland Kirk and Hubert Laws were early jazz folks ... Hubert Laws did a show with Jean-Pierre Rumpal ... and blew him off the stage ... JR couldn't improvise much ... and Hubert would not let up! The various classical pieces were also better done by Hubert, as JR stuck to the score, and showed a lot less personality and ability! Ian Anderson would probably throw him off the stage for buffoonery!