I cannot save at all either.
I have wasted almost 4 hours and played through the first section of the game 3 times, and have grown to hate it now.
I have a Fallout4 folder, but the game seems completely incapable of saving the game at all.
Another issue I and many have found is that we can only play in windowed mode as the launcher will not save the pref files, unless it is run as administrator, but as the launcher starts the game itself, there is no way of doing this for the actual game, only the launcher.
For one of the most eagerly anticipated games in the last 10 years that I can remember, Bethesda have done an extremely poor job in aiding those on PC who cannot even play the game.