Bee nests, female protagonist... isn't it perchance
King's Bounty: The Armoured Princess?
(Except it's not an RTS, came out much later than what you have specified and lots of details don't match; but anyway, thought I'd mention it.)
[Edit] A quick search at MobyGames yielded this game:
http://www.mobygames.com/game/windows/tempest__
A side-scrolling RTS, according to the tags and description, lots of female characters.
You can also try finding your game in the
female protagonist game group.