The disgraced founder of the X-Men, Professor Charles Francis Xavier, was introduced as a wise and beloved mentor to the original five X-Men, but over the years he has experienced a profound fall from grace. From being considered a terrible father to his son Legion, to secretly getting a team of young mutants murdered, Xavier has a whole slew of sins inside him. Now considered a monstrous villain, by both humanity and mutantkind, Xavier's time as de facto leader of Krakoa's Quiet Council led to the Professor's final fall, a place he might never recover from.
In a secret attempt to defeat Orchis and Enigma, Xavier "betrayed" the X-Men by siding with Orchis and murdering a number of humans, and act that horrified humanity as well as his mutant students. This was later revealed to be a fake out crafted by Charles himself to keep his precious X-Men safe, but Xavier is determined to keep this a secret from everyone on Earth, so he can remain humanity's true villain.
X-Men #35, the final comic of the Krakoan Age, saw Wolverine attempting to murder Xavier for his crimes against the world, before Magneto stopped him. From deep within a prison, Xavier continues to protect his "children," but his legacy is forever tarnished, and he may never be considered a hero again, especially after his years of moral lapses.
Xavier Has A Shockingly Long History Of Ethical Failures
From secret teams to enslavement, the Professor is no hero
While Charles debuted as a kind father-like figure to Cyclops, Jean Grey, Beast, Angel, and Iceman, the peace-loving Professor was later revealed to be capable of terrible things. On a personal level, Xavier has always been a terrible actual father to his son David Haller, the X-Man called Legion, ignoring him and denying him the Xavier legacy even as recently as the fall of Krakoa. Yet Xavier's true sins run much deeper, and involve mayhem, death, and betrayal. Xavier's two most terrible crimes before the Krakoan Age - that we know of - are his enslavement of the artificial intelligence Danger and the deaths of the Professor's second X-Men team.

Cyclops Was Justified in Killing The X-Men’s Founder
Professor Charles Xavier may have founded the X-Men, but his death at the hands of Cyclops was more earned than anyone would like to it.
Charles knew that the Shi'ar AI he used to build the X-Men's Danger Room was sentient, and he explicitly chose to ignore it's personhood and force it into servitude for years. Eventually, the rogue AI, Danger, broke free of her conditioning and nearly murdered all the X-Men. Years earlier, as revealed in the shocking Deadly Genesis (2006), Xavier sent a second team of X-Men - Petra, Sway, Darwin, and Cyclops' half-brother Vulcan - to rescue the original X-Men from the monstrous Krakoa, and they all perished. While it was later revealed that both Vulcan and Darwin survived in space, this reveal was the true beginning of the end for Xavier's time as a hero, and the start of his real descent into villainy.
The Professor Is Attempting To Atone For His Many Past Sins
But, can Charles Xavier ever truly be redeemed?
The final straw that broke Charlie's back was his destruction of the Space Force Frigate Agnew, killing several high-ranking human officers, in an attempt to win favor for his mutants in the eyes of Orchis. However, the "What Charlie Did" arc of X-Men Unlimited Infinity Comic revealed that while the Agnew was destroyed, no humans were killed, with Xavier psychically implanting the officers' identities in the public eye. Now labeled the Butcher of Krakoa - and in many ways, rightfully so - Xavier is attempting to atone for his many sins before and during the Krakoan Age by remaining a secret martyr, allowing himself to be kept behind bars with the world believing he is a monster.
Charles Xavier did not debut as a very complex character, instead showing up as the tough but loving mentor to the X-Men. However, the past several decades have shown Xavier's complexities, moral failings, and dangerous pride, as the world witnessed the former Professor tumbling from grace and becoming yet another evil mutant.