For most people it's simply habit, and that exploration is more fun than 'turtling', but there are legitimate reasons to colonize. The mine vs automine situation you've already noted, but there is also that population growth is faster for small populations (max 10%, min 2% for any pop 100 million or larger), 'civilian trade' is only conducted between different populations, and that forward bases (for fuel, maintenance, and munitions) are needed and easier to create/support with a population (though it can be done without). Most of the other reasons for colonization have been done away with by successive editions of the game, but there is also that it's a lot easier to tell another empire "MINE!" with a population present, than with a bunch of ships orbiting various rocks.
That said, I've frequently played (or more accurately, NPR'd) races that squat on their homeworld and bring resources to it. Asteroid miners, automated mines, sorium harvesters, freighters and jump ships go out, harvest whatever minerals are available, and carry everything back to the homeworld where all the industry & population are located. They also feature an extremely cautious exploration strategy, strip-mining a single system for everything that can be gathered before moving into the next.
