Many horses don't like their ears being touched, some develop the phobia just from being low man in the herd but most often it is caused by abuse. Many big breeders who don't have time to train foals, they just churn 'em out, will often drag them by the ears. Also reaching your hand up quickly toward her ears can be a really threatening position, it could be a smack or a pat, she'd rather not stick around to find out.
This being said, it doesn't matter what the cause is, it's a problem, especially if it inhibits your ability to tack or groom her. My suggestion is to practice touching her. Put her on a lunge line in an empty arena, make sure her focus is on you (at least one ear on you). Start somewhere she's comfortable, probably her shoulder or back, and just rub her, make it a pleasurable rub not a fly tickle or a smack. Most horses enjoy a good scratch behind the withers or on their chest between their front legs. From your starting point work your way to areas you know she's comfortable, rubbing her all over. Watch her body carefully, if she looks uncomfortable with a spot move away from it slowly then slowly back toward it until she's comfortable. If she moves quickly away from you or acts out aggressively (with a snap or stop) immediately send her out for a lap or two on the lunge line, that's not acceptable. When she's back in work again where she's comfortable then moving on toward less comfortable areas. Work your way up her neck toward her ears, the moment she looks concerned move back away and tell her it's alright, continue this until you are touching her ears all over. Practice this a while every day and I'm sure she'll quickly overcome this fear.
Good luck :)