I don't participate in the fishing tourney very often, so I can't exactly say if I feel bad when Chip eats the fish. Since I don't do it all that often but personally I don't mind but it's probably because i'm used to it I guess!
One aspect of Animal Crossing that I have always appreciated so very much is the continuous support of veganism, whether intentional or not, with the Franklin character and everything. I just think it's really sweet and a good message to put out to little kids about animals.
That being said, I can appreciate the humour in him eating your fish. After all, he can't help it!