I have noticed that my rear wheel is always considerably muckier than my front one, after a wet commute.
Why should that be? They both travel the same distance and terrain. I assume this is a common experience.
Bike has mudguards.
As mentioned in the other answers, there could be several reasons that your rear tire is always muddier than the front after a wet commute.
The front tire splashes mud on the rear of the bike.
There is more weight on the rear tire, causing it to sink deeper into mud.
Your power is being transferred to the rear tire, creating more friction than on the front.
You're probably using your rear brakes, causing your rear tire to slide. If so, it's probably better to use more of the front brake.
One more thing... the mudguards are probably not keeping your wheels and tires clean. They're there to keep you from getting splashed.
The rear tire may be dirtier that front tire, regardless of mudguards or rain, because it is closer to the chain. The chain is a dirt magnet and some of it will splash to the wheel by the mere proximity to it. For instance look at the chain stay on the chain side, it is always dirty just because of being next to the chain.