The explanation for the bogus vaccine-autism link is a constantly shifting target. As noted, both the MMR vaccine and thimerosal have been blamed, and the anti-vaccine movement happily gloms onto both explanations despite the fact that they are completely unrelated. That the various theories never really cohere doesn’t seem to give the movement pause. Blurring dark but vague threats, anti-vaccine activists blend them into a miasma through which no given study can hope to penetrate. Uncertainty is good for stoking fear.
When studies show that the MMR vaccine doesn’t cause autism, and when the original study suggesting a link is exposed as a fraud? It must be thimerosal! Other studies show no association between thimerosal and autism, and thimerosal isn’t even used anymore? The combination of all the vaccines at once is the problem! Produce evidence to support the safety of the current vaccination schedule, and the boogeyman simply adopts another form.
Because much of the evidence in support of vaccines comes from the Centers for Disease Control and Prevention, detractors seize on corruption as an explanation for studies with findings contrary to their beliefs. The anti-vaccine movement affords the CDC roughly as much respect as you’d typically give cardsharps and second-rate grifters, and anything the CDC produces is dismissed out of hand. But even if the CDC were a hotbed of malign pharmaceutical industry influence, that doesn’t explain why large studies demonstrating the safety of vaccines come from places like Denmark or the United Kingdom, where the CDC doesn’t have a lot of pull.