If money was indeed stolen (and wasn't just misplaced), and if you were keeping the safe key on you, then it had to be an inside job. Even if someone made a dupe of the safe key, they couldn't get in without your room key. And while I'm sure it's possible, I can't imagine a non-CM being able to both break into your room AND the safe quickly and undetected.
You should've been more aggressive with Disney's security. If they had security cameras set up within the lobby, they would be able to see who went in your room. If it was just someone in Housekeeping, they should be able to see if anyone else has complained about missing items when he or she was their Housekeeper and build a case of circumstantial evidence from there. If anyone else had access (if say, Maintenance went in to fix something), OR if a non-CM managed to open your door, it would show on the tape.
At the very least, I agree that the police should've been called. Even if they determine that $325 isn't enough to warrant a full investigation, Disney security's edict seems to be less "Protec the guest" and more "protect the corporate reputation."
Here's something I wonder, and if anyone's in Hotel Management, perhaps you could answer this question...
All the resort rooms that you a magnetic card-style key...is there any way to determine which key was used and when? Since they usually have those little lights on them to determine if a lock is unlocked or not, they have some kind of power source, yes? And if they have a power source, do they have any kind of memory? And if there is a memory, could it be determined who unlocked a door and when? Whether it's the guest's key (which would only open that door) or a CM who might have access to all doors?