I hear ya.
I sense it must be more than that too. I reckon our deepest desire is to live, so it may be that we fear realizing we don't deserve to live. We're afraid of discovering ourselves because we may find that we are monsters, that we are bad. The way we generally view the world in terms of morality is
life = good
death = bad
In our eyes life should be good, it should strive to be good, it should have as much good and as less bad as it can. That could be why people who see themselves as 'bad' (without value or with little value) feel like they don't deserve to live.
deepest desire -> life
deepest fear -> to lose life
we fear ourselves because -> we might find we deserve to lose life
Being rejected may make us feel like we lose value, we become more bad and less good. It contributes to the "realizing we're bad" part, so I could see how some people feel like the reason we don't accept ourselves is because we fear rejection.
However, what is bad? And what is good? Does morality exist? Etc... In my opinion, for example, there is no 'good' or 'bad', there is just existence/essence, so in my case I don't feel like I'm either bad nor good inside, rather, I just exist as I am. For example, I feel like when I am angry I'm not 'more bad' than when I am generous, rather, it's a different expression of the way I am – the 'ying' to the 'yang', as I mentioned the other day :) Beautiful in its own way. That's why exploring the nature of reality could make us realize that there is no good nor bad, everything just "is", so everything has value -> no reason to fear ourselves.
In other words, we can't fear ourselves because we can't find a monster inside. We can't find a monster inside because the distinction between 'the monster' and 'the non-monster' part of ourselves and the world (distinction between bad/good) is just an illusion. If we explore ourselves keeping that in mind, we will see that we have value regardless of how we are, because we are only existence in its purest form – nothing to fear :)
Some religious beliefs may create turmoil inside a person because most religions make clear distinctions between what is right and what is wrong. They segregate the person and make them neglect, vilify, be ashamed of, not accept (etc) some aspects of themselves. They may make them feel that a part of them is wrong, that it has to be changed, which makes self-acceptance much harder. So yeah, I feel you....
How to overcome the fear, though? Well, what has worked for me is two things:
–Realizing the truth
–Letting go of desire
With regard to this, buddhist teachings are very helpful.
Buuuut... this is only my humble opinion Hopefully it can help you in some way.