A recently developed model to describe proton collisions from molecules involving basic atoms such as hydrogen, carbon, nitrogen, oxygen and phosphorus (H, C, N, O, P) is extended to treat collisions with multiply charged ions. The ion-atom collisions are computed using the two-center basis generator method (TC-BGM), which has a proven track record of yielding accurate total cross sections for electron capture and ionization. The atomic net ionization cross sections are then used to assemble two models for ion-molecule collisions: an independent atom model (IAM) that follows the Bragg additivity rule (labeled IAM-AR), and also the so-called pixel-counting method (IAM-PCM). The latter yields reduced cross sections relative to IAM-AR near the maximum, since it takes into account the overlapping nature of effective cross sectional areas. The IAM-PCM for higher-charge projectiles leads to strong reductions of net ionization cross sections relative to the IAM-AR method, and is computed directly for projectile charges Q = 1, 2, 3. The scaling behavior of the IAM-PCM is investigated over a wide range of energies E, and at high E it converges towards the IAM-AR. An empirical scaling rule is established which allows to reproduce these results based on proton impact calculations. Detailed comparisons are provided for the uracil target (C 4 H 4 N 2 O 2 ), for which other theoretical as well as experimental results are available. Data are also shown for targets such as water (H 2 O), methane (CH 4 ), adenine (C 5 H 5 N 5 ), L-valine (C 5 H 11 NO 2 ), and the nucleotide dAMP (C 10 H 14 N 5 O 6 P). Based on the scaling model derived from the IAM-PCM data it is shown how the experimental data for uracil and water bombarded by multiply charged ions can be reduced to effective Q = 1 cross sections respectively, and these are compared to proton impact data.