Yub Nub suited the original trilogy as an ender. It feels out of place with the prequels. The Star Wars trilogy was essentially a feel-good story about overcoming impossible odds, defeating injustice and the power of friendship. Yub Nub is a bit silly, but considering you are watching a giant party where teddy bears are dancing with characters you have grown to love over the years as they celebrate their triumph, it somehow suited it. It fit with the plot and tone of ROTJ, and the trilogy itself.

Yub Nub never had much widespread hate against it, and had little to do with the reputation of Jedi. In fact, Victory Celebration got a lot of criticism in 1997, because instead of the feel-good ending song you had some melancholy Enya type thing that is even more out of place musically. It fits the additions of the SE and the expanded story of the prequels, but since a lot of people hate those things in the first place they care little for the accompanying track that replaced the original.