While I don't like Bethesda interfering with the way I want to play my games, and don't buy the argument that as paying customers we're not within our rights to criticize their decision, I think this may be an issue with your installation, not with Bethesda's game. As mentioned above, please check whether your plugins.txt at C:\Users\<username>\AppData\Local\Fallout4 is set to read-only. Next, open it up and place an asterisk before each ESP and ESM except for the main Fallout4.esm, e.g.:
# This file is used by Fallout4 to keep track of your downloaded content.
# Please do not modify this file.
Fallout4.esm
*AwesomeMod.esm
*AnotherAwesomeMod.esp
The mods should load up with no problem for you now.