scared cat

one of my cats is terrified of everything and i don't know how to fix it. he spends almost all day in my/his room. the top of the cat tree is the only other place where he feels safe. he's sneaks around behind the furniture or right next to the wall if he's walking around the house, never out in the open. any noise will make him run to the room to hide. he freaks out most of the time when my family gets close to him and either runs away or crouches in a corner if there's no way to flee. he does that with me too but not as severely and i'm the evil person who takes him to the vet and has given him meds. he only runs away from me half the time i see him. he doen't wear a collar because he freaks out when he wears it. we have a closed off patio but he rarely ventures out there and then only if i go outside too. but in my/his room he comes and cuddles and isn't scared at all. also, he appears to be the more dominant of my 2 males.
i don't know what to do to get him to be more confident.

It just takes time and patience.
I have a beautiful white kitty, Pearl, that is now 9 years old. She was rescued from an abusive home at 5 months and spent 7 years mostly in the closet or under the bed. She has recently become a fairly normal kitty that will come for scritches and tummy rubs. She got a little less shy and timid over the years, but she has blossomed now.
She was terrified to go out, but now she has moved into the well shed attached to the back of the house, and spends a lot of time napping in the sun. She plays with a possum and a fawn that live in my back yard, and loves running around in the rain.
She went from a shy, terrified kitty to a happy girl, but she did it on her terms. She still does not really like the other cats, but that seems to be working itself out as well.

How long have you had him and how old is he? Has he always been like this? If you haven't had him long, it might just be that he's not used to the new environment yet. If you've had him awhile and this in new behavior, then it could be something happened to him and he needs to go to the vet. If you're sure nothing's wrong with him medically, you might try a feliway diffuser to help calm him down some.

i've had him since he was about 6 weeks old and he's around 2.5 years old now. when i had him and his littermates as fosters he was adventurous. it started about a year ago and keep getting worse. i don't know if anything happened to him as a kitten because he was abandoned. the only other i can think of that was bad was him getting out once and getting scared but that was before he was even a year old.
it doesn't bother me that he's not outgoing but i worry about him being scared so much

Have you moved? Has anything else in your life changed? My girls were traumatized when we moved house 2 years ago and only now are they starting to get back to being boisterous etc. These things take time and much patience (and have to be on your furbaby's terms) but you will get there

I agree, any changes with some cats takes a LONG time to get over (some just take them with a grain of salt). Even moving the furniture or getting new furniture can freak some cats out. Do you know what happened to him when he got out that one time? Maybe something in the last year triggered a memory or something and caused him to get timid.

How old is the other cat? Is he still the Alpha? If he is that young, maybe they were just letting him "think" he was the Alpha because he wasn't worth fighting since he was so young, and now that he's older they are letting their presence known. I've seen that before in barn cats. The older cats tolerate a kitten "strutting their stuff and feeling like they are all that", then once they are full grow...BOOM! Reality hits.

All I can suggest is a safe place for him to feel comfortable in until things settle down. Is he peeing or pooping outside the litterbox? Is he still eating and drinking? If so, most likely it's just something he has to work out on his own with your help.