So, 500 million metric tons sounds like a lot, doesn't it? But there's the fact that it's getting dumped into an already big system: the atmosphere at large.

Let's check it out it percentage terms. According to wikipedia, the mean mass of water vapor in the air is 1.27 * 10^16 kg. To get the units correct, that aviation contribution is 5 * 10^11 kg. Dividing the latter by the former, we find that the annual commercial aviation water vapor represents 0.004% of the mean mass of water vapor.

That's rounding error.