So I go to colonize my third planet, and since there are native inhabitants, I figure I better be ready. I have the money ready and buy a market to please the inhabitants on turn one and have money to buy a tank on turn 2 (with more citizens in transit). But they revolt and take over the planet on the first turn.

Part of me says "Hey, that's kind of neat. Realistically speaking, natives might well rebel." But then, as far as I know, the game gives you no realistic tools for preventing this. And it seems like a very strange focus for gameplay anyway.

I feel like I am looking at some very strange occurrences in this game, and I really am starting to wonder, am I just seeing some rare stuff by happenstance, or is that the way the game is?

Bring some troops in transport ships along with your colony ship?

Well you already prepared a couple of things to prevent rebellions, but these are realy rare on the first turn as unrest is tied to probabilityy: there is a chance that a pop gets unrury, and if tehre is more of them then what you can handle, rebellion occurs.

I think, that what you have seen is bad luck. If there is a 25% chance that a native pop gets upset, you have a 1:3 chance that you will loose the planet in the firs turn

What can you do to prevent these, I mean additionally to that what you have mentioned?:
1. Send in additional colonists via transports together via the colony ship. You have 2-3 pop in turn 1
2. Send in tank, or Marauders (if you are playing Gremak). The later are excellent at putting down unrest
3. Research tech that decreases the naturaly agression other races have against you: there are two levels of this tech and the second one nullifies it completely
4. Send in an empty transport with the colony ship, and ship the natitves off the planet right off the bat (if they can be shipped)
5. Enslave the natvies (if possible) and force labor them or use them as reasearch mice

Note that pops have varous special attributes, so some natives are inclined more towards unrest then others and there is one that is even immunie to moral effects (you can rejoice if you find them )

Possible but not normal; USUALLY if you get a market that buys you plenty of time to deal with unrest. Sounds like you just had really bad luck in this case. Which species were the natives?

-Will