The dogs have jobs, too, so they need to be able to get out to catch their lift.
My dogs are trained to pee outside, stay off beds and so forth, but they come inside to bark at and attack the cats. I made them aggressive so they could be "guard dogs". I was sort of hoping they'd only be aggressive to non-family members, but apparently not.
I think if you want your dogs and cats to stay separate and yet all still have jobs, you're going to have to micromanage a little more by specifically locking/unlocking their doors at appropriate times for them to go to work. This is what I do with most dogs in the game, so I can keep them outside during the day (I'm sick of them peeing on everything) but still let my sims take them on walks off the lot. I only unlock one door for the dog to walk out of the backyard with the sim.