Reddit mentions of Temperament: The Idea That Solved Music's Greatest Riddle

The answer is in the history of temperament. It's not so much an arbitrary thing someone sat down and did but the endpoint of an evolution of keyboard instruments that used to contain far more keys to the octave to accommodate commas in a phythagorean temperament. If you really care enough you can read Stuart Isacoff's Temperament.

In the meantime, while I'm not one to ever tell someone to just take something without questions, this is one where you should probably just drink in what you can with giving into the conceit of the keyboard being "imperfect" in some way.

From a practical standpoint it's also helpful to get your bearings at the keyboard.

For the sake of your sanity, don't think in whole and half-steps all the time. It's good to use this to understand how scales are formed, but you really shouldn't think this way overall. If you're thinking of scale strucutre you'd probably be better off thinking in term of key signatures and intervals. If you're trying to think in half or whole steps to add up to things like a 4th in a given key, you're doing it the hard way.

Perhaps if you give me a better idea of how the keyboard gives you trouble I could give you some more specific mental tricks or ways to think of it from a different angle that makes it less difficult for you.