You're definately not the only one with that problem, so don't fret
All guinea pigs are different, and all you can do is be patient and caring and loving.
I had a guinea pig named Buttons (r.i.p) and she was extremely friendly and loved being handled, etc which was great but my other piggie Mittens is completely different, she runs if you come near her and kicks her legs when you finally can pick her up, but after a little while, she settles down and likes being cuddled, but then when you put her back in her home, she runs for cover again lol.
My other two guinea pigs again are different, Socks seems to be more adventerous and is a bit of a busy-body and always comes out to see whats going on and at meal times she waits by her bowl with her two front paws in it and squeaks like crazy, she lets us hand feed her and lets us stroke her and tickle her under the chin, but when we go to pick her up she runs into her pigloo or does laps really quickly so we can't catch her lol, but once we have her in our laps she is very content and happy - but it's always a struggle to catch her lol. Bows is very shy and hates being picked up, she'll squeal and kick and bear her teeth, catching her takes a while, sometimes i let her be because she seems stressed but most of the time i persevere because I think in the long run it'll be good for, when I do have her in my lap she stays very still and always has her eyes wide open, but I think in time she'll get better, it does take time though...I don't think mine will ever like being picked up to be honest, that's just how they are
I think also to keep in mind, that we are sooo much bigger than them and it must be daunting for them to have big hands coming towards them lol and like other people have said, they are prey and it's their instinct to behave that way, just keeps handling them and give them lots of cuddles, and even try tempting them with some food, I try enticing them with half a grape occassionally and that usually works.