Can you make money from your settlements?

Yes, you need a special perk, Local Leader level 2, as told here and build stalls.

Local leader perk level 2 requires and gives :

2 CH 6, LVL 14 You can build stores and workstations at workshop settlements.

How you generate income :

Q: How do you earn money from your Settlements?

A: Learn Local Leader perk and then construct the different stalls in the Stores section

You got to collect the money from the settlement workshop, confirmed here :

Go to workstation storage and scroll to misc. You should see caps there when you get paid out

and here :

I just checked my workshop. if you hit transfer then scroll to misc there should be bottlecaps in there. I just found 50. you might have to wait a bit longer though

and also here

You were answered, it does indeed go into that settlement's workbench