In your average 5g gravel tank, there are many times more nitrifying bacteria in the substrate than in an average, adequate filter. (I wish I could find the TFK thread where a member actually did the math).
There is so much more water flow through the filter that the bacteria in there convert more ammonia than the relatively poorly fed bacteria the substrate.
Regarding substrate, there are subtle reasons having to do with plants that make a lot of sense to me. But not being a plant person, I'll stick with my bare-bottomed, cycled tanks.