In their minds there are no humans on the surface worth saving. All have been tainted my radiation which would affect future generations.
Pure bloods (you the backup and your son the primary) are very important genetically to the Institute.
I believe they make synths in hopes of rebuild the world faster, with an army of Gen 2 workers, this makes much more sense to them than trying to organize the people living on the surface right now.
Let's face it 80% of the people and 99% of the animals we meet as the SS are not worth saving. In fact we kill them on site. The Institute has to love us whether we join or not, haha.
FEV and supermutants was the Institutes first attempt to purge the surface and that failed. FEV experiments have been abandoned but many super mutants still live on.
Now Gen 1 and 2s are sent to the surface to collect, by any means, supplies, tech, raw materials, etc.
Gen 3's were sent to spy and disrupt any group trying to organize.
Coursers are their soldiers.