That's beginning to sound a lot like a conspiracy theory. An equivalent of what you're saying is that lung cancer researchers make up their results because they want to kill the cigarette industry. That's not their goal; their goal is to do research, uncover connections, and add to human knowledge about cancer. They don't have anything substantial to gain by hurting the cigarette industry, cigarettes just happened to be heavily connected to cancer.
And they address your points in the article. They're looking for CTE specifically, which has specific markers, which they state is found in vastly higher percentages in football players compared to the general population. However, the director of the study even cautions toward taking the data at face value because "there is tremendous selection bias" (her quote) due to brains being donated by those players or their families who saw visible symptoms. She's saying to take it with a grain of salt. They have 1200 brains yet to analyze too. However, they point out that if those 1200 come back negative (highly unlikely), it's still about 9% of former players being diagnosed with CTE as a baseline value. That means at the very least one guy on offense and one on defense on the field is likely to develop the disease at some point. But the point of the research is figuring out exactly how it develops, whether it can be reversed, when to advise players to retire, etc. If we ignore there is a problem, then you won't see any innovation in the study of the disease and development of equipment to prevent against it. Football as a sport or professional institution won't be killed and there is no precedent or evidence to suggest that will ever happen. I think people are overreacting.