In solving the wave equation $$u_{tt} - c^2 u_{xx} = 0$$ it is commonly 'factored'
$$u_{tt} - c^2 u_{xx} = \bigg( \frac{\partial }{\partial t} - c \frac{\partial }{\partial x} \bigg) \bigg( \frac{\partial }{\partial t} + c \frac{\partial }{\partial x} \bigg) u = 0$$
to get $$u(x,t) = f(x+ct) + g(x-ct).$$
My question is: is this legitimate?
The partial differentiation operators are not variables, but here in 'factoring' they are treated as such.
Also it does not seem that both factors can individually be set to zero to obtain the solution--either one or the other, or both might be zero.
Yes, this logic is totally legitimate. In the language of linear algebra, we have two operators $A$ and $B$ and the wave equation is $$AB \psi = 0, \quad A = \partial_t - c \partial_x, \quad B = \partial_t + c \partial_x.$$ Since $A$ and $B$ commute, they may be simultaneously diagonalized, i.e. there is a basis $\psi_i$ where $$A \psi_i = \lambda_i \psi_i, \quad B \psi_i = \lambda'_i \psi_i$$ so the wave equation becomes $$AB \psi_i = \lambda_i \lambda'_i \psi_i = 0.$$ This is satisfied for $\lambda_i = 0$ or $\lambda'_i = 0$, so the set of solutions to the wave equation is just the union of the nullspaces of $A$ and $B$.