I don't doubt for a second that hockey is a factor here, but I have a very hard time seeing it as the biggest factor, for a few reasons: (1) hockey's popularity varies widely across the state. In Roseau/Warroad, the Iron Range, the Duluth area, and the wealthier suburbs, hockey has been and remains very popular, but that's not nearly the case in most of the rest of the state. You don't hear of a lot of DI/pro hockey players coming from places like Alexandria, Mankato, Winona, Willmar, or New Ulm, for example. In 2015-16 (most recent stats I could find), 13,542 boys played HS basketball in MN, while only 5,792 played hockey. (2) hockey is more and more a rich kid's sport, with the advent of year-round play, and this is bringing down the number of kids playing, especially in the city and in inner-ring suburbs. Thirty-five years ago, Columbia Heights, Richfield, and Cooper all had competitive high school hockey programs; none of them even field a team any more. (3) There are exceptions - as mentioned, guys like Zach Budish and Anders Lee, and had they focused on it guys like Nick Bjugstad, Paul Martin, and Blake Wheeler might have had a future in football - but a lot of the high end hockey players Minnesota produces would be unlikely to be successful in football due to size limitations. Zach Parise, for example, is listed at 5'11' but is probably shorter than that; Jake Guentzel weighs about 160 and it's hard to envision him in big-time football.
As is the case with most things, there isn't a single cause for this perceived problem; instead, there are a ton of contributing factors (among them the unfortunate fact that youth developmental programs are poorest in the inner city where the most African Americans reside, a lack of a year-round football culture, single-sport specialization, and yes, hockey, among others).