Chances are it's not because it's windy, it's because of atmospheric pressure, although I'm not sure about the mechanics of why the water level should drop.
Here, in England, we sometimes get storm systems causing a tidal surge down our East coast. Effectively, this means, because of low pressure, that there is less air pushing on the ocean which means the water expands ahead of the cold sector of the system. As the water expands, with tidal pressures included, as well, it causes all sorts of problem, of which, the Thames Barrier was created to prevent.
Your toilet? Wind is created by a difference in pressure. You can see this on your nightly weather forecast by looking at the lines they stick (they're called isobars) the tighter they are the windier it will be.
Next time the toilet level goes up or down look at the weather forecast. If you are under a given pressure system, then that's why the water goes up and down.
The answer? - it goes down because atmospheric pressure is high, or is rising.