C3PO is funny and Jar Jar isn’t.
A big part of humor is contrast, and C3PO is an excellent study on contrast; he is completely different from his buddy R2D2 and is himself a contrast, wanting to be helpful and purposeful but being an oblivious doofus.
Jar Jar contrasts with nothing. He has no counterpart, and he himself is just a clown.
The point about Jar Jar being designed to appeal to children is actually a pretty apt one, and if I may draw a comparison, consider how insufferable Sesame Street become when it started to revolve around Elmo. Elmo doesn’t serve any comic function recognizable to an adult, the way Grover, Kermit, Ernie & Bert et al. all did; they appealed to children but used comedic techniques that appealed to the grownup as well. (Many of Grover’s scenes with the constantly irritated blue-skinned muppet are absolutely Grade A TV comedy.) The relationship between C3PO and R2D2 is quite similar in tone and theme to Bert and Ernie, the former being prissy, easily irritated and more clueless than they themselves believe (another similar pairing in a kid’s show would be Squidward and Spongebob) while the latter is cheerfully determined and prone to antagonizing the former, often without really wanting to.
Who’s Jar Jar’s counterpart? There is none; he’s just an idiot.
I don’t think that’s the full extent of it; there’s also the generally displeasing CGI look of him. But that lack of basic comedy science is most of the problem.