By default, Beyond Compare detects many languages based on the dot extension on the filename, including C languages, Cobol, Delphi, Java, Javascript, Perl, Python, SQL, and visual Basic. More can be downloaded from Scooter Software. If your file is in one of these languages, Beyond Compare will automatically mark any comments as unimportant.
When you look at your file, you will see red and blue color highlighting. The red is to show you the really significant things, the important differences. The blue color is to show you things that are different but that you might not care about, like different whitespace, different capitalizations, and, as we are interested in here, different comments. If you really want to not see the blue, unimportant differences, you can turn the highlighting from blue to nothing at all by hitting the MINOR button.