You are correct given your understanding of 'net force', both when the proton is in the centre and off centre. So for instance if the proton were closer to one side, the flux would be higher at a given point on that side of shell compared to a given point on the opposite side. It might appear then that it would exert more pull on that side. However, because the far side has more surface area, the combined flux on the far side perfectly (as it turns out) balances the smaller and closer and higher flux side. (Note: this is valid for a sphere, not a circle.)
That said, I don't want people to misapprehend that this kind of 'zero net force' translates to no force at all. Rather, the proton is exerting an inward force on the shell. What prevents the shell from collapsing inward is its tangental velocity, which, given the shell's mass, translates to a balancing outward centrifugal 'force'. By orbital mechanics, it is the shell's constant tangental velocity that requires that it is at a fixed distance from the proton. This is the reason for the proton's "preferred" position in the centre, as I've mentioned before. So in summary it is the attractive force of the proton on the electron shell, combined with the tangental velocity of the shell, which fixes the proton in the centre. The shell theorem can take a rest.