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In my limited experience that's the key right there.  I don't handle Thor any more than necessary for routine care.  He's always been a tad bit afraid of me, simply because I don't handle him or allow him in my space.  He's a great roo with no aggression.  His "brother" that I handled alot was quite a bit more aggressive.
Sometimes it's still a toss up. My first set of chicks got handled a moderate amount, but as they grew up I let them keep to themselves. One roo turned out unreasonably mean by the time they were 16ish weeks I knew he was a goner. His "twin" brother is still protecting my flock today!!
My current youngsters are hitting about that age. I haven't handled them much at all. They come up to me for treats though. One black sexlink is a peacemaker and kind, his "twin" brother is mean and comes at me! Raised the same way, and similar genetics, but it's a toss up.
PERHAPS in my limited experience, the dominant roo doesn't feel the need to challenge me, but the 2nd in command roo thinks he can get ahead so he takes it up trying to get ahead of me? I know typically the dominant hen is  less mean than the ones in the middle-ranks because she doesn't have to constantly prove herself. These two particular BSL cockerels are pretty closely matched, the mean one puffs up and tries to challenge the nice one VERY OFTEN, but they don't actually get into knock-down-drag-outs.
I agree that it's a toss up, but here's some food for thought...
You have a young cockerel that doesn't have an ounce of aggressiveness in his blood.  What happens if you baby and handle him alot?  Nothing, except that you have a really nice sweet roo that likes to be babied.
But what happens if you have a cockerel that's prone by genetics or bad blood or whatever to be mean and you handle him alot?  You've removed his fear of you.  One less obstacle for him should he decide to become aggressive.  
After seeing what I saw with my two roos, I will never baby a rooster.  I love on my hens tons and leave him to do his job.
Just saying.