Are you wearing a "raider or leather" harness? That is an actual armor/clothing piece like the Postman Uniform and it will make you look "naked".
You need to wear the Postman Uniform for example, plus a chest piece, 2 arm pieces and 2 leg pieces. Then you are fully clothed and armored.
Only certain clothing can be worn under armor. Try a military outfit, or longjohns. Most suits will not work.
^This
I prefer the Army Fatigues as I've gone with Combat Armour.
I did want the Silver Shroud suit under my armour but I can't.
I also have my settlers wearing armour pieces to distinguish who is doing what. But I have no spare clothing for them. So it's like a weird semi-nudist camp.
Yea that and if you have 5 armor pieces equipped, it will take them off, when you switch to something that doesn't allow them (like my Hazmat suit).
@ Danger Close: LOL at you semi nudist camp
Or http://www.nexusmods.com/fallout4/mods/745/? allows you to equip armor pieces on top of your clothing. Some clipping, naturally, but it can be done.
Another alternative is the Road Leathers. I use this combined with the 5 piece leather armor to make it look more realistic. I think it looks better than the fatigues or ... egggh ... long johns.
You cheeky dog...!!
Then you can just ring the bell and have them all come give you a little fashion show...