If there's one consistent trait superheroes possess that endears us to them, it's that they're not infallible. Comic heroes don't fight because they know they'll win - they do it because they know someone has to, and they're willing to put their life on the line to be that person, and to help others.
Even Superman - who by all means is stronger and better than regular humans in just about every way - is capable of being taken down by someone completely underpowered, given the right circumstances.
Without the very real chance that even the strongest heroes could be beat, there'd be literally zero stakes to the comics they're in, and as such, zero reason to actually pick the comics up and read them.
And there's only one solid way to make it appear as though said heroes could be defeated; namely, by having them get beat. Showing significantly weaker opponents taking the likes of Batman and Wonder Woman down proves that, even for the most powerful superheroes, any opponent can become a genuine threat - even if it's only temporarily.