I always liken it to trying to free a rabbit that has its leg stuck in a fence (or whatever): YOU know that you are there to help it; YOU know that you don't mean the rabbit any harm. But all the rabbit sees is that you are big and scary and could easily hurt or kill it, and you are approaching it while it is vulnerable and cannot escape.
Do you get offended when the rabbit is afraid of you? Are your feelings hurt when it panics as you reach for it? When it tries to bite you? And when you manage to free it, do you get angry when it runs away from you as fast as it possibly can, without so much as a thank you?
Of course not - or, if you do, you need to grow up. The rabbit has no way of knowing what your intentions are. All it knows is that it is trapped, and that if you decide to attack it, it will likely die.
Obviously not a perfect analogy, but still. Women cannot read minds, and our predators look no different from any other man. Approaching a woman when she is alone or otherwise vulnerable is going to freak her out, and it doesn't matter if you're just a big teddy bear on the inside. You are big and scary and you are approaching her when she has no means of escape should you attack her.