1. In baseball and hockey, there were professional sports teams around for years before the modern versions of the NHL and Major League Baseball were established. It was almost inevitable that some of these would continue functioning as “minor leagues” even after the major leagues were established.
2. Football and basketball were different because of an unusual historical fact in the development of these sports. Up until somewhere around the post-WW2 years, college football and basketball were actually more popular than the pro leagues. There was never a network of small professional leagues for these sports because a normal “career” for these athletes involved a college scholarship, a couple of years in collegiate sports, and then moving on to something else for a career.
What happened post-WW2? Television.
You are right that college football was more popular pre-World War II, but the fact is there were professional football leagues clear back into at least the 1920s. The actual fact of the matter is that gridiron football at any level did not even become widely popular until World War I, so it actually took a relatively short period of time between 1918 and 1945 for the game to develop.