Wow another SDMB post where someone is confused by normal everyday human interactions.
Someone hands you something you want, you say “Thank you.” It’s really just as simple as that.
Depending on the size of the workplace. I work in a vet clinic with a 7-person staff, so my actual boss writes out the checks by hand–it would be really silly and pretentious to then hand the checks to someone else to distribute. Hell, sometimes if I’m not going to be in on payday, my boss puts my check through the mail slot at my actual house.
Every week my manager goes to every employee and hands them their pay envelope (containing their check or notice of direct deposit) and personally thanks them.
If you don’t offer a “thank you” for such service, you are instructed to read every book by Miss Manners in one sitting.
When I was getting an actual check every two weeks, I never said thank you, whether it was handed to me or just left for me. It’s MY money, I earned it.
I certainly thanked that boss for good working conditions, respect, fair treatment, the opportunity to work, etc. But not for what I’d already earned.
I’m definitely a jerk though. 
I can see the case for politeness and traditional cultural exchanges.
In this exact situation, I have said “thank you”. It indicates I have it in my hand and they can let go, that I see the social situation correctly of handing off an object, and I am damn grateful for my job and that the boss actually fulfilled his contractual obligation, all of which I am thankful for.
Correct communication in this situation was one of the things I learned in Boy Scouts (which I generally disliked) that when handing off an ax, the person handing off did not let go until “thank you” was issued so that it would not fall on someones foot.
The resistance to saying “thank you” for a paycheck merely identifies to the boss who the first assholes are that need to be let go when times get tough.