You know, like the extra 5 health on SCVs and the 1 extra supply given from a Command Center? At least with units like the missile turret it makes sense for it to be a bit better as far as attack since it can't shoot ground (unlike it's counterparts).
Juan Manuel's answer is the correct answer in the general case. You have to look at each race as a whole to evaluate balance, not the individual specifics. A 1v1 comparison between an SCV and a probe (or a zealot vs. a marine, or a cannon vs. a turret) may make it seem like one race has a "bonus," but SC2 isn't a game of SCVs vs. drones, it's a game of race vs. race.
As for the specific cases:
My point is not that "Terran bonuses are actually not as good as Zerg/Protoss;" my point is that each race has lots of unique strengths and liabilities, lots of units and upgrades that are great at some things and weak at others.
The point of SC2 strategy and tactics is to discern these strengths and weaknesses, and use them to one's best advantages to win the game.
Balancing 3 complete different races is not easy.
Keep in mind that they are not bonuses, they are traits from the race; the Zerg and Protoss also have things the other races do not; just as an example, regeneration for the first, shields and Warpgates for the second.
If the races didn't have these differences you'd end up basically with the same 3, just with different skins; kind of the orcs and the humans on Warcraft 2.