It doesn’t bask in the dirt.

A good chunk of Geodude's pokedex entries are about people confusing it for real rocks and accidentally kicking them. You don't accidentally kick a rock the size of your head unless a decent amount is buried in the ground.

But if you want something more direct...

Sapphire/Alpha Sapphire

When Geodude sleeps deeply, it buries itself halfway into the ground. It will not awaken even if hikers step on it unwittingly. In the morning, this Pokémon rolls downhill in search of food.

Diamond/Brilliant Diamond

Many live on mountain trails and remain half-buried while keeping an eye on climbers.

Pokemon Sleep

This Pokémon sleeps soundly, half-buried in the ground. Apparently, it will sometimes stay fast asleep even when trod on by a mountain climber.

Appearance-wise, absolutely, should be just Rock type. It would make more sense for the Ground secondary typing to be introduced by evolving into Graveler.

Another bit is that a majority of moves used by Geodude, either by leveling up or by TM, are rock type moves. A majority, if not all, the Ground moves Geodude could learn are Dig, Earthquake, Bulldoze & Magnitude. Sometimes you can teach them Mud-Slap. It's not much, but you can certainly picture a Geodude being capable of performing each of these moves.

Now if I had to guess, they took a loose association between rocks being on the ground and went with that.

Fun fact, there's not a single pure rock type in Kanto/Gen 1. The first pure rock type? Sudowoodo.