How you handle it can depend on your house layout alot. For me, I have a sliding door right into my backyard with a kennel in the corner right by the door. When it's muddy outside, my dog goes out, does her thing, then when she comes in she gets to take a 15 minute nap in the kennel (don't tell Goose) to dry off before I let her out to roam the house or resume her nap on the couch. Having them kennel up to dry off also keeps her from doing the in and out routine that's common when it's nice out. But she's learned when it's raining or wet outside, looking out the window might be better than actually going outside and having to go into her kennel when she returns.
It's why crate training is important in young dogs. My dogs have never hated their kennel, they prefer not to be in there or course but it's not a big deal for them to be in there if they have to be. As I mentioned in another thread, I'll often find my dog laying in her kennel with the door wide open. Even though she'll refuse to go out when it's a mess outside and she knows she'll have to kennel up when she comes in.