/Originally/ there was no Thief. Just say'n.
But, yeah, in AD&D, they were the 4 classes, and the others ('cept the oddball Monk & Bard) were sub-classes of 'em.
And, that didn't really change much in 2e (they became four class groups: Warrior, Wizard, Priest, & Rogue), so for about 25 years, that was just the way it was, and... ...it became a tradition.
But, what the traditional cleric & magic-user do - cast spells - is essentially not that different. And what the traditional fighter and thief do - use mundane skill (fighting's a skill) - is really not that different, either.
You could probably take D&D down to just those two 'classes' - magic-user and skill-user; Mage & Hero, perhaps - and get all the remaining PH-in-some-edition classes and sub-classes and one-off-class-in-one-supplement-one-time classes by just applying various Templates to them.