In literature, as in life, cages are usually wildly unpopular. They're small, they're cramped, they're locked. Honestly, what's to like?
It follows, then, that the characters in Rats hate cages as much as the rest of us do. Each time a character is in a cage, he or she has her freedom restricted and he or she absolutely hates it. Captivity? Always a bad thing in Rats.
Never is this clearer than when the rats are locked up behind bars in NIMH. However, because our rats are brainy, they understand that the cages don't just prevent them from moving around like they would like to; they also prevent them from thinking and knowing as much as they would like to:
Just the fact that it was a cage made it horrible. I, who had always run where I wanted, could go three hops forward… and that was all. But worse was the dreadful feeling… that we were at the mercy of someone we knew not at all, for some purpose we could not guess. (15.44)
Horrible is a good word for what has happened to the rats. But in this quote the cage is also linked to not knowing about what is going to happen, which is even more horrible. Think about it: when you're in a cage, you can only see so much of what's going on in the outside world. Whatever's going on beyond the three feet of space right in front of the cage door is entirely out of reach. That's got to feel pretty frightening.
Mrs. Frisby, our heroine, also has a run in with a nasty cage. Being placed in a birdcage is particularly terrible for Mrs. Frisby because she has a whole bunch of information that she needs to share with the rats about their impending deaths at the hands of those mysterious government exterminators. Her entrapment is heightened by the sense of suspense. She is also prevented, quite literally, from taking care of her kids by the "vertical bars, smooth and no thicker than match sticks" (25.6). By chapter 25, it's pretty clear that cages in Rats = Very Bad News.