The important thing to remember is that it's not a very big thing. That is, even Planetary Annihilation, which had a $99 price and didn't give extra goodies, had a backlash at first. The people who complain loudly about these kinds of things are a very very tiny minority and they do it on multiple games.
The backlash against PA was a thousand times more justified than it is for GalCiv3. PA offered almost nothing more than the base game for this price, basically justifying the higher price with the, ahem, "privilege" of helping the developers make the game.
With GalCiv3, I'm not paying for any of these alpha testing "privileges". I am paying to preorder the game and its expansions, knowing that I will help testing the alpha without having to pay for it. That's a huge difference.
The problem, however, is one of GUI . It is NOT immediatly obvious that those $99 are for the game and its expansions, and neither is the justification behind it. People usually don't dig deeper, because that would take a whole lot of time; first impressions matter and steam really isn't helping you here.