This paper studies the effect of channel coating hydrophobicity and analyte polarity on the gas detection capability of a microfluidic-based gas detector. Two detectors with two different channel surface coating combinations (resulting in different levels of hydrophobicity) are fabricated and tested against seven analytes with different polarities (methanol, ethanol, 1-propanol, 2-pentanol, acetone, pentane, and hexane). A feature extraction method is utilized to compare the discrimination capability of each of the fabricated detector. The analysis of the combined feature space presented for both detectors reveals that the Euclidean distance, which is an indicator of the device discrimination capability between different gases, between the feature vectors of the two sensors are greater for non-polar gases compared to those obtained for the polar ones. This shows that the analyte discrimination in microfluidic gas detectors is not a purely diffusion-based process, and there are analyte/channel surface interaction parameters involved in enhancing/impeding sensor selectivity. To understand these effects, the surface free energy of each fabricated channel was determined. It is shown that the difference between the solid-liquid surface tension values estimated for the two channel surfaces is higher for the non-polar analytes as compared to the polar analytes. This effect along with the low diffusion coefficients of non-polar analyte magnifies adsorption of the analytes in the diffusion-physisorption process, resulting in a greater difference in Euclidean distances between the features obtained from the two detectors responses against non-polar analytes as compared to the polar ones. This shows that the choice of the detector's channel coating material plays a key role in the selectivity of the device between different gases. As a result, non-polar channel coating surfaces are suggested for better classification of the non-polar gases, and it is shown in the cases of polar gases changing the coating surface has less effect.