A lot does depend on the snake, but it does take a little bit of thinking about how snake behavior works.
These are reptiles. They are not cats or dogs, they don't have a big enough brain to be like a cat or dog. Their brain is the equivalent of our brain STEM. They're not dumb...they're just not at all like us, or most mammals, mentally.
So, that being said, these are not animals with the large mammal brain that deals with social interactions. These aren't social animals, period. It boils down to conditioning them to handling - to teaching them that hands and handling does not mean they are going to be eaten, hurt, or bothered in any other way except that they are out and moving when they would rather be hiding. Taking them out of their cage tells them that the hiding spots they have in their cage are obviously not as secure as they had believed, so why would they want to go back into a place full of hidey holes that you can get into?
Of course, some snakes really don't seem to mind being handled. Some snakes will sit calmly on a lap while the owner watches TV, while others cruise around but never go far. Some snakes will only feed if their owner is the one offering the meal. But, some snakes seem intent on striking at people any chance they get, some eat from whoever tosses the mouse in, and some seem like they are just waiting for their chance at freedom the second they get out of the cage.
Basically, know your snake. Be aware that it doesn't "enjoy" being handled the way you would enjoy a backrub, but some snakes don't seem to mind handling much, if at all.
Like Ballman said - if it's eating regularly, shedding well, and defecating normally... then whatever you're doing can't be all that bad.
I handle almost all of my breeding snakes regularly, and they do just fine. 
~jenny
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"Polysyllabism in no way insures that what you're saying is actually worth being heard." - Blake (an e-friend of mine)
"I have never made but one prayer to god, a very short one: "O lord, make my enemies ridiculous." And he granted it." - Voltaire