Its less about what he was 'accused of,' more about what the Wanli Emperor stood for.

I am not a Ming Dynasty historian (though there are plenty) so I'm by no means an expert on Wanli or the period, but I am familiar with him. Understanding a little about him will help us answer this question. Wanli is a very controversial emperor in Chinese history. Contemporary sources make him out as hard to work with, uninterested in state life, and generally just kind of a ditz, although I imagine some of those claims are embellished. His rule is sometimes blamed, or placed, as the downfall of the Ming, though hindsight is 20/20. Why is the downfall of the Ming particularly bad for contemporary Chinese in the 1960-70s? Because the Qing were not ethnically Chinese, they were Manchu. Furthermore, the Qing were targeted heavily by Chinese propaganda because it was the dynasty they dealt with when they were kids or their parents/grandparents were; they stood for 'feudalism,' that ancient evil that kept the people oppressed.

Now, what feudalism is in Chinese Communist theory is pretty complex. Even many Chinese in the 1920-40s producing these anti-Qing documents really had no universally agreed upon understanding of what was feudal and what was not. Generally, they agreed Confucianism was overall, as well as Buddhism, but also more practical things such as landlordism and footbinding. But there were arguments about what else was and was not feudal. Was a peasant making sandals in a black market to sell for some extra money feudal, or at least capitalist, or was it part of their ability to freely govern themselves like a truly communist society believes in? Mao at least believed that underground black markets were capitalist evils (also called feudal), and that is another topic which was dealt with in the Cultural Revolution.

After the founding of the PRC, ideology calmed down as the mainland assumed a Maoist state. Many Chinese citizens in the 1950-60s had the benefit of being able to prove themselves as true patriots, anti-imperialists, or loyalists to the Party through participation in WW2, the Great Leap Forward, etc. When the next generation which grew up in the mid-60s-70s came of age, they came into a Chinese society which left them disenfranchised. They had no previous record of being able to 'prove themselves' as loyal to Mao, because no major campaigns had been launched after the GLF. The economy was in shambles due to the aftermath of the GLF. This was a group of young adults who felt somewhat betrayed by Party elements. Conveniently for Mao, he was also in the midst of a power struggle in the 70s and this is really when his cult of personality reaches its zenith.

So back to Wanli. Recall that I said things such as landlordism, imperialism, and Confucianism are all elements of what the communists generally agreed were 'feudal.' Wanli pretty much embodied all this. Like the other emperors, he was a Confucian. But more importantly he was seen by post-PRC communists as a symbol of allowing China to wither into weakness. He allowed not just his own dynasty to fall, but to fall to foreigners. This can, and was, being interpreted as complacency with imperialism. He allowed China to fall into the hands of regressive foreigners who re-enforced traditional cultural elements such as the oppression of women, the following of Confucian ideas, etc.

So why Wanli, and not any other emperor? There are a fair amount of emperors buried in mausoleums throughout China, and you can visit the Ming Dynasty Tombs today in Beijing as a tourist. Well, Wanli's tomb happened to have been just recently excavated in 1959. Additionally, the excavation itself was pretty controversial. It was handled poorly, and a lot of material remains were lost. Bodies were ruined due to improper techniques. For as life-giving as oxygen is, its also very destructive to remains. This section of the Mausoleum where Wanli and his empresses were buried are also pretty expansive and flamboyant. As you're probably aware communists generally enjoy destroying expansive and flamboyant properties because they see it as representing the use of wealth to further personal goals rather than for the betterment of society. It all made the Dingling section ripe for destroying.

Zealousness combined with ambition made young Red Guard members salivate at the idea of destroying Wanli's remains. Not only did he represent the feudal past of China, but he wasn't even a good emperor. He allowed China to descend into chaos after his death, and for that he needed proper punishment. And it was more personal for these Red Guard members, whose grandparents/great-grandparents were the ones left to deal with the Qing dynasty and all it embodied until 1911. Even in its aftermath, the fall of the Qing left nothing but ruin until the CCP established the PRC in 1949.

As a final note, the location and history of the Ming Tombs made them much more convenient for raiding. The tombs are located only about 20 miles away from the center of Beijing, whereas other tombs in the area are 70+ miles away. Throughout the tumultuous period of the 1920-40s, the Ming Tombs were pretty well preserved, whereas various Qing Tombs had in the past been plundered and looted by various warlords.

In conclusion, his remains were 'denounced' and then burned mainly because he was a symbol of this idea of what remained of feudal elements in Chinese society. Of course the Wanli emperor being complacent with foreign imperialism is pretty radical, as he wasn't even alive during the fall of the Ming but these were radical times. Red Guards were pretty much looking for any excuse to destroy what they saw as the remnants of feudal society. Confucian, Daoist, and Buddhist icons/temples were also heavily targeted.

Sources:

Son of the Revolution. Liang Heng and Judith Shapiro.

Revolution, Resistance, and Reform in Village China. Edward Friedman, Paul Pickowicz, and Mark Seldon.

To Dig or Not to Dig: Qianling Mausoleum in the Spotlight Again from China Heritage Quarterly.

City of Heaven Tranquility: Beijing in the History of China. Jasper Becker