I agree this isnt the best idea but its not uncommon. When I have seen them its been with the books and left in the trunk area, either an access compartment or with the spare wheel out of normal sight. It makes sense why they do it but yes it can be a theft issue.
Car thefts and ones who break into the car are typically two different types of people. Most thefts occur by people who already know how to steal the given car so the key would be irrelevant. Most break-ins are by people looking for easy items to sell and often wouldnt go through the trouble of hanging around the car for long or want the attention stealing it would bring.