Could definitely be ear mites, she could have an infection, does she live in a wet area or have lots of hair inside her ears? I'd check with a vet.
Another thought I had - is she out with other horses? Could she have nagged her ear on something? Normally if a horse is feeling afraid for any reason, or defensive in any way their ears and their underbelly are the two places they'll defend to the end.
If a Vet clears her and says there's nothing physically wrong it sounds like you need some ground work.
How I'd do it:
Start by rubbing her shoulder or neck and rub in a way that feels good and relaxing, not like a fly tickle or an invigorating scratch. Rub up and down her neck slowly, with her on lead standing quietly, not on cross ties or loose. Watch her signs very closely, rub in the direction of her ears, the moment she gets nervous tell her it's alright and go back somewhere more comfortable, repeat this process each time moving inches closer. Move away until she's calm then work into her less comfortable places. Practice this over her entire body too. When you get to touch her ears be quick about it, do a quick rub over her ears then back to rubbing softly on her neck, don't put stress on it by making it a slow painful process of touching her ears. Rub her neck up to the base of her ears then swipe your hand over then back to soft rubbing where she likes it. Eventually she'll get over this if there's no physical issue.
A more assertive way of doing this, if you think her ear shy problem is caused out of disrespect not fear:
Have her on a lunge line. Practice rubbing her neck, gently go towards her ears, if she reacts by pulling away or being fresh send her out and make her work. Practice her backing, yielding front and hind ends. Work her bum off until she realizes it's easier to stand quietly for her ears being touched than to have to work so hard.
Try whichever of those methods you think more applies to your horse - Assuming there is no physical reason, you should consult a vet though.