It may not be so.  Some cats just are timid.  

When I first got Pi, he was typically rambunctious, but since he's an
indoor cat now, he's become unused to noises and ructions.  If I so much
as sneeze, he'll go hide.  The smoke detector goes off every morning when
I make my breakfast (it's the crib's way of keeping me humble) and Pi
invariably hides under the bed.  The doorbell ringing is cause for a
panicked flight into his favorite hidey-hole.  

I'm fairly sure he's never been abused in any way.  He's just a timid
boy.  

Chak

Poor Boyfie, it's so sad, especially as he can't tell you. :-(

Hopefully, in time BF will gain enough confidence that he'll enjoy
chasing things when you throw them. But, some cats are just timid and
easily frightened. Of my two former strays, I'm positive LB was
abused. How else would she know what a fly swatter was well enough to
be terrified when she sees one hanging on the wall? Over time she's
gained enough confidence to do things she wouldn't think of doing for
the first couple years she was here - like getting on counters.

OTOH, I'm think Spotty is just timid. She doesn't act like she's
afraid of getting hit, just doesn't like anything above her head -
which  suppose may well be an instinctual thing. She enjoys being on
my lap, but doesn't seem sure if she should jump up on her own. So,
she comes up to where I'm sitting and reaches up and asks, but won't
make the leap up herself. Then she flinches away when I reach to pick
her up. Once she's up it doesn't take any time before she's purring
and kneading away.  I'm hoping that some day she won't flinch when I
reach down to pick her up and pet her.