We study multiple ionization in proton collisions with water, methane, and ammonia molecules using an independent-atom model. Previous work on total (net) capture and ionization cross sections is extended to treat the multiple-ionization channels explicitly. We present the theoretical framework to treat charge-state correlated processes within the independent-atom-model approach, which uses the geometric screening introduced for different molecular geometries and orientations. A comparison of results is made for the target molecules ${\text{H}}_{2}\text{O}, {\text{CH}}_{4}$, and ${\text{NH}}_{3}$ with an emphasis on $q$-fold electron removal. Coincident measurements of produced molecular fragments can be used to estimate this quantity. We find very good agreement for the model calculations for the water molecule, where data exist for $q=1--4$. For methane we observe reasonable agreement for $q=1,2$ and for ammonia only for $q=1$, i.e., the experimental data show little support for a direct multiple-ionization channel in the latter case.