Precisely. As the EM-wave passes through a circuit, it induces a current within the circuit that overloads it. This happens because a circuit is a closed loop, and the charges in the circuit will experience a force as the EM field changes, thus causing the current in the circuit to change. The change in current vs. change in time is proportional to the area enclosed by the loop (among other factors), and the rate of change (flux) of the EM field. With a strong enough flux, like say, from an EMP, a circuit can easily overload and be ruined, or the electronic device attached to the circuit can be rendered useless as well.
Now I'm not totally sure about how the nerual connections in our brains work, but if they make closed loops, then I think they're simply too small and not able to carry enough charge (or carry charge in quite the same way) as a typical circuit, so they don't respond to EMP like electronics do.