How do I make a NPC protected by the guards? Essentially I am trying to make some civilian NPC's for my first mod, but I am not sure how to make it so you get a bounty if you attack them. Do I have to add them to a particular faction?

you'll have to check out how vanilla guards handle it, but i believe its handled through a faction, if not you can run a script on the NPC to make sure, read this and related pages, it will probably tell you.

http://www.creationkit.com/index.php?title=GetCrimeGold_-_Faction

Add them to a crime faction I believe, take a look at vanilla npc's and see how its done its probably the best bet you add them on one of their specs tabs. There are other settings like don't report crimes against other members etc (the thieves guild uses this one iirc) but a regular npc should tell you what you need to know.