Why didn't Captain America have a cartoon in the 90s?

It might not seem like it now that the character has woven himself into popular culture, but Marvel Studios was worried about how the global market would receive Captain America. In the Marvel universe, Captain America is a pivotal member of the Avengers and a beloved hero in his own right. In the real world, Before the Marvel cinematic universe, Captain America was a d-list superhero- unless you were from the 40s like Steve Rogers. Outside of a few video games and cartoon appearances, the mainstream had no idea who Captain America was. 

In the 90s, Marvel created a bevy of animated shows featuring their characters. For many fans, this animated universe was Marvel's first stab at the MCU concept. Through the groundwork laid by those cartoons, Marvel helped embed the popularity of several key IPs in the minds and hearts of a new audience. Out of all the major heroes, Captain America and Thor were the only characters that didn't have their own series. In the video linked above, YouTube's Owen Likes Comics explains what happened to Captain America's series.