We do it because the words 'king' and 'queen' had very different meanings and still have different values. 'King' comes from the Anglo-Saxon cyninge which originally meant supreme (elected) military leader with an implied sacral element. Her or His Britannic Majesty is still the titular head of the armed forces, to whom military personnel swear allegiance and Defender of the Faith. 'Queen' comes from Old English cwean (and/or Scots Gaelic wheen?) both of which meant litle more than 'wife'.
Eventually using the word 'queen' only for the wife of a King is pretty typical of English, where two words which were synonymous in their root languages are subsequently endowed with different meanings and values, and are consequently useful to unpick for their implications about culture, politics and gender. An obvious one is the way we use Anglo-Saxon words for animals, and Norman French ones for meat: cow/beef, sheep/mutton. I have read - in an A level English Language textbook no less - that this was a reflection of the superior culinary standards the Normans introduced. That's both a simplification and a cliche. The people shovelling the animals's shit in the barn were more likely to be the invaded, and the people scoffing the meat in the hall were more likely to be the invaders. The two mingled of course, but the fact that French became the language of the fine dining and Old English the language of the farmyard is reflected in the language we speak now.
The problematic nature of having a Queen as King, when the words are still laden with different values and implications, is why the term 'Prince Consort' was invented for Victoria's Albert. It ws too risky to call him a King, even a King Consort. It was one of the reasons why ELizabeth I never risked diluting her precarious authority and status by taking one of the many husbands who was mooted for her. HRH The Duchess of Cambridge - Princess Kate - will, in due course, will be called Queen, despite being a commoner, if Young Baldy Big Ears becomes King. It's already been publically stated that the calm, competent and well-adjusted Duchess of Cornwall will never bear that title if Old Baldy Big Ears becomes King. She's never sought the title of Queen (of Hearts or anything else), and there is a depressing assumption that residual public sentimentality about the dead, kitten-faced, neurotic, cripple-hugger would make it very difficult for her to do so.
It would be better - well, less problematic - to suggest calling Lizzy Two 'King', rather than calling it a 'Queendom' while she's Head of State. Which she is, as the elected PM still has to go through the ceremony of asking her permission to form a government, and she opens Parliament each Autumn. It is not an entirely ceremonial role, and could, in extreme circumstances, be a much more interesting one.
Ther cultural assumptions around gendered titles for royalty can be seen in any pound shop, with the amount of pink, sparkly tat retailed at and for little 'princesses'. Even the least politically aware father is unlikely to call his son his 'little prince', and there aren't blue, sparkly outfits for boys in the shops. 'Prince' still retains a veneer of power. 'Princess' is either a term of endearment (harmlessly affectionate or problematically patronising, according to one's poloitical outlook) or actively pejorative, as in 'Jewess Princess'.