the reason I find it interesting is that I have heard, several times in fact that all species of reptile found in Idaho are Protected species, including Rattle Snakes and yet this little PDF says that any of the listed species can be possessed, live or dead by anyone over the age of 10 with a current hunters license and have a bag limit of 4 per species per person.
I think they are using "protected" in a less than accurate manner. They are no protected in the sense that they are considered threatened or endangered, but covered as are many species simply as animals you can just shoot willy-nilly (for lack of a better description) unless they pose a threat of some kind or have specific regulations about them, such as the limit you noted.
Without seeing the specific text or law, that would be my best explanation for what you describe. Several states have some similar statutes.