The Sorcerer's/Philosopher's Stone was removed from Gringotts to be placed under the most impenetrable of protections at Hogwarts under Dumbledore's custody. But it seems clear Dumbledore took protections which could have been impenetrable, and deliberately made them less so, such that at best they would only slightly slow down anybody trying to access the Stone, rather than just plain block them.
For example, after the Devil's Snare, you have a locked door enchanted such that it cannot be opened by any charm or other means except its own assigned key. That's a great protection, potentially an impassable barrier if the key is not available.
But the key is then left right there in front of the door in the same room.
At least the key is flying around the ceiling. But there are broomsticks right there in the same room, too.
The room with the fires front and back—that could also have been a solid defense—deadly fires that cannot be passed through unless you drink very specific potions tailored to each particular fire's properties.
Except that those potions providing safety are put right there in the same room.
At least, perhaps, they're surrounded by other bottles, some of which contain poison. With no way to know which bottle is safe, that could still almost be a solid protection.
Except that a piece of paper with a logic puzzle detailing exactly which bottles are which is put on the table with them.
Dumbledore always had reasons, and those reasons were always virtuous. What was he up to, deliberately weakening the protections in this way?