Cory - Like you stated, there is substantial resistance with the heavy water droplets in the air.
Also, a tire may slip a little [hydroplane] and thereby incur a loss.
How about wind? That is a contributing factor.
Your MAF sensor may be influenced by water vapor to read a bit differently, and maybe use more fuel.
Your exhaust pipe is much cooler, and will condense the exhaust gas and make it harder to push out - resulting in a net loss of engine efficiency.
There is additional cooling in the engine compartment, and if a cylinder head is cooler, it uses more of the available power from the fuel to heat the head [trying to reach homostasis] - this results in a loss of fuel efficiency.
If because of drag you have to give a slight bit more throttle, maybe your computer ignition timing and fuel map goes richer and allows less ignition advance, which would result in another loss of MPG.
Cooler tires may have more rolling resistance, as well.
There will be a bit of extra drag on the engine because of headlights and wipers being on.
Now, we have to figure out answers if someone's MPGs go UP in the rain!