Part of the reason is that the Mongols themselves are not shy about what happened. The Secret History of Mongols is a document that is nearly contemporary with the original conquests and outlines their brutality. But sometimes conquerors boast. Consider the monuments erected by the Egyptians asserting they won the Battle of Kadesh, which they did not in fact win.
But we have external validation of the Mongol impact on the world’s human geography. The human die-off was large enough that it may have left an ecological footprint to increase carbon uptake from forests that grew because fewer people were around to cut them down! Additionally, there is lots of circumstantial evidence that the Mongols replaced some of the genes of people they killed.
If you want a thorough modern overview, I recommeend Genghis Khan: His Conquests, His Empire, His Legacy. If you want, “actually Genghis Khan was good”, then Jack Weatherford’s Genghis Khan and the Making of the Modern World.
A bigger question is how we should judge Genghis Khan in relation to his time. Julius Caesar in Gallic Wars claims hundreds of thousands of deaths. Other ancient historians argue for millions. These are likely exaggerations, but they illustrate the fact that ancient war was brutal, and the Mongols were basically a hunter-gatherer people who had recently taken up nomadism. Their morality and ethics were primitive, to say the least. In t he 18th century the highly civilized Qianlong Emperor ordered the genocide of the Dzunghars.
I think the clear reason why the Mongols and Genghis Khan are held in such ill repute is that they were the greatest and most explosive of the barbaric eruptions from the Eurasian core. They were Atilla the Hun simultaneously assaulting the Four Corners of the world. They quickly created the largest land empire in the history of the world and therefore wreaked havoc from one end of Eurasia to the other. The Mongols finally collapsed the distinctions and distances between disparate portions of the Eurasian “rimland” civilizations. They were the ones who brought Roman Catholic Alans to Northern China and sponsored a flourishing of Buddhism in Iran for several decades. The consensus is that the Hui Chinese Muslim community derives mostly from the Mongol period when they imported Central Asian Muslims as a “middleman minority.”
Many books of history that are macro-focus use the Mongol Empire as a watershed because it destroyed so much and created a new “world system” which persisted long after the Mongol Empire as such was no more. To understand the “Great Divergence” and the early modern breakout of Europe, one has to understand the resurgence of rimland polities in the wake of the Mongol shock.