Given that the entire adventure was a dream, the magic of the shoes was merely a subconscious exit from the dream.
Remember, Glenda did not know the power of the slippers. She merely said they must be powerful if the Wicked Witch of the West wanted them so badly. Even the WWotW didn't know their full power, it wasn't until she got shocked by them that she realized they couldn't be removed until the wearer was dead.
It's possible Glenda later learned of their ability to teleport the user, although the reality is that it really didn't matter. Essentially, this is a case of "Why not just fly the eagles into Mordor?"; There'd be no point to the story if that happened.