No bashing, not a dumb question and welcome!
Phone manufacturers add their own skins to Android; Samsung has TouchWiz, HTC has Sense and Motorola has the skin formerly known as Blur. It's how they differentiate themselves from each other.
The Nexus phones have no skin, they are straight up Android, vanilla.
Here is an article comparing them (not Nexus/Vanilla) from Gizmodo
. That compares ICS, not Jelly Bean but you get the idea.