I think it just depends on how a cage is used, if it is large enough to give enough room to move around freely and has lots of environmental enrichment, be that food related, toys etc and the animals have a lot of human interaction and time out of the cage then no I don't think it's cruel.
My guinea pigs are kept in a cage but it's 6 ft by 2.5ft so they have a lot of room to run around, they are housed in a herd which is very important for their mental well-being and they have a constant supply of hay to munch as well as chewable toys and hideys.
My cat is also an indoor cat-we moved and unfortunately live by a very busy road. She has lots of room ( we live in a 3 storey house) and places to sleep in the sun and supervised access to the garden. I'd much prefer that to her being out on the road and being hit by a car, if we move to a quieter area in the future then I'd think about letting her out.
I do however worry about a lot of rabbits living in this country, it makes me cringe to see the tiny hutches for sale in our local pet shop as part of a 'rabbit starter kit', most of them would be too small for 2 guineas let alone a single rabbit and a single rabbit is also unfair.
Our pigs used to be outside, in a nice big hutch but I felt too guilty about them out there when it was cold and used to spend all evening in the winter checking on them and the heat pads I put in the hutch
They have time to run around out of the cage but with the exception of my older girlie, don't enjoy being picked up so I don't cuddle them all that much as I figure it would be more for my benefit than theirs!
ETA-a pic of my piggies cage from when I fed them their veggies last night
https://i241.photobucket.com/albums/ff73/pinklizzy_photo/AA4615EC-CE90-49F0-AC26-752F9933E097_zpsaakcfv9v.jpg