On one hand, this is due to poor science journalism. The media loves nutritional research because telling people what they are doing wrong generates clicks. It is very easy to sensationalize. "A small correlation between celery and colon cancer in a specific population from a specific region" (or whatever) in a scientific paper becomes "Celery slowly killing you, Harvard researchers prove".
One the other hand, this is how science works. We do experiments, get the results of those experiments, and try to make the best use of the data we have. Usually, the truth is much more complicated, but there are always bigger and more complicated experiments which need to be done to understand this more complicated truth. This happens all the time in all fields of science, but isn't as visible to the broader public because most research isn't all that relevant or interesting to non-scientists.
It is REALLY hard to design good (ethical) experiments in nutrition. The scientific consensus now is very different than what it will be in 10 years, because we will have more data and higher quality data. This will allow researchers to continue to incorporate more complexities and nonlinear effects. So you're right in that "linear thinking" is not ideal, but a linear model is better than no model.