Two things in tandem ended Lott's career in the senate leadership. First, Lott had a long history of support for and association with segregationist and white supremacist groups in the South. Not in some distant past but in the year's just before his downfall. (He was also a staunch opponent of virtually all civil rights legislation. But that actually didn't distinguish him that much for many other Southern Republicans of his generation.) To a lot of us at the time it was always a bit of a mystery how someone with his record could have risen as high as he had. This was all widely known in Washington, DC but it was by common agreement overlooked and excused. (In many ways, because of this, it was a scandal of official Washington -- as much as Lott.)
Then one day, Lott said this remarkable thing -- if only the candidate of segregation (Strom Thurmond) had been elected president in 1948, we'd have avoided all the problems we've had in recent decades.
Most other politicians could have walked away from this remark with the claim that they just hadn't thought through the implications of the statement. The problem for Lott was that almost everything from his past suggested that he knew the implications exactly and believed them deeply. To put it more baldly, too many past statements and actions made it clear he was a supporter of white supremacist politics and segregation. Suddenly what official Washington had always ignored was open to intense scrutiny and his days were numbered.
Folks can make an argument for Reid's punishment on its own terms; but the Lott analogy is laughable.