Consider the following scenario. "Bad chemical compound" (which is a close variant of "good chemical compound") exists in a concentration of 1% when your total level of "good chemical compound" exceeds Y.
Therefore a high level of "good chemical compound" correlates with the harmful effects of "bad chemical compound". Does "good chemical compound" cause the harmful effects? No. Does it correlate? Yes. Now "good chemical compound" is the evil compound that must be lowered.
Now imagine that there is a product that has a high degree of "bad chemical compound". So suddenly there are lots of people with low levels of "good chemical compound" but they suffer from the very same harmful effects that higher levels would predict! "Bad chemical compound" has been found in the product itself and therefore the product was banned.
However, the fact that "good chemical compound" isn't the problem hasn't been recognized because detecting "bad chemical compound" in products is very easy due to the extremely high concentration but difficult (read expensive) to detect in the blood due to the much lower concentration. So the only "reliable" indicators that exist must be based around correlations because measuring the "bad chemical compound" isn't done.
That was a long winded way of saying oxidization of cholesterol causes inflammation and the formation of plaque in blood vessels. Detecting oxidized LDL is possible but almost no lab does it. Instead you get spurious correlations, the most reliable of which is HDL to triglycerides.