They hated the “your battery level is low” and “you should take a break” prompts from her that, for whatever reason, Nintendo loved to shove into their games around that period. Not Fi. People really liked Fi. Quite a bit more than Navi at the very least and maybe not quite as much as Midna.
No...people hate Fi herself.
Fi has a cool design, and she has a good introduction, a very good theme song, and a nice (albeit unearned) farewell at the end of the game. And that's all she has going for her.
Those don't make up for her flaws..
Not only does she pester you about batteries and taking breaks, which is already bad enough.
She also tells you how to do every single thing no matter how obvious. There are times it's very clear what you must do, but she jumps out of your sword to say "master there is a high probability you should [do thing]" before you can just do it yourself. It's genuinely awful, and it's the main reason people hate her so much.
She has literally no personality by design because she is made to be robotic. At the end of the game she tells you she thinks she feels close to Link, but it means nothing because she never expressed any emotions over the story, she could be replaced with an encyclopedia about the enemies and it wouldn't make a difference.
If Fi had a personality like some other popular Zelda characters, maybe more people would put up with her or even grow fond of her. If she didn't interrupt so much, people would at least not resent her. The idea of a spirit in the sword is a good one, it's just better for the spirit to shut up and not be telling us every 10 minutes to dowse or change batteries or use the new item on an obvious puzzle or whatever else.