Yes, I wouldn't want a Trek show to depend on selling toys, either. That would almost certainly generate episodes that I would not enjoy watching. GL and YJ were very good, though (but they were apparently financial failures, and I wouldn't expect a new Trek series to be ordered under similar conditions).
I'm sad to admit it, but you have a good point there. However, cartoon shows being tied to how well toys sell is not a new issue. In fact, it goes back to the same era the original Star Trek animated show was made in. An animated show based on or depended on toy sales can still attract a larger audience than just the 6-10 crowd. Take a look at something like Batman The Animated Series from the early 1990's. I gurantee toy sales from that show were being look at. Yet, that didn't end up affecting the quality of the show. And it's not alone. My point being is that it can happen, but the stars have to be aligned just right and the powers that be from the studios have to give some leeway to the creative forces.