A combination of factors:
(a) It’s a matter of intimacy. Thou/tu/du is commonly known as “second person familiar” and who is more familiar with you than God? And in true intimacy, respect, honor and love are present regardless of word form. Late Modern English, of course, has done away with “thou” and adopted “you” as the all-purpose 2nd. person singular. However when you contrast it to a language with familiar/formal versions, you have for instance how in Spanish, addressing God as “usted” would sound presumptuous, as if, you’re not on first-name terms!
(b) Language evolution. In the old, old form of many European languages, there is only one 2nd-person singular root, and it usually is the one that later evolved into the “familiar”. Even kings would be addressed as “thou” if ever addressed directly(that is very important). Again with the Spanish comparison, to this day the verb-conjugation tables in a Spanish grammar will give tú/vosotros (thou/y’all;) ) as the single standard 2nd-person verb forms.
However, during the evolution of the languages thru the Middle Ages and Renaissance, it became customary that in “formal” situations, say at the Court, a “courteous” form of address would be adopted. The courtly persons would use the “Royal We” and would not be addressed directly in 2nd-person-singular as a person just like you, but would be addressed in the plural form: thus “You”; or German “Sie”, using the plural verb forms. In the case of kings, of course, they’d address each other as countries (“Greetings to our cousin, France”)
Spanish took this a step further: instead of “tú”, the couteous person would address others as “vuestra merced” – “your grace”, using the plural form of the 2d-p-fam-possessive – and the 3rd-person verb form would be used. That phrase with time evolved into “usted”, the modern Spanish 2nd-person-formal.
The major Reformation-Era translations of the Bible into English (the KJV) and Spanish (the Reina/Valera) share the pattern of using what was then considered “classic” forms, using “Thou” even when referring to royalty and the Deity (even though by then they would not dream of actually addressing real live royalty in the familiar in everyday speech.) This, quite probably, because the Hebrew, Aramaic, Greek and Latin texts do not use a second-person-formal either. Add to that centuries of Christians, Jews and Muslims praying and handing down scripture in the classical languages, and you get it being well established that God is on “Thou” terms with humanity. Being above petty considerations of rank-inflation, he’ll let the kings and prelates argue over nonsense like who should addres the other as “Your Most Excellent Righteous”.
