I agree in general that they're often misused, but "just" and "simply" do have a place. Specifically in place of "only" or "instead", or to set up a subjective comparison.
A: I'm going to do X, Y, and Z.
B: If you just do X, we'll meet the requirements.
A: I tried X Y and Z to fix my problem.
B: You can simply reinstall the IDE.