The NY Times said so emphatically in their editorial today:

"This page (NY Times editorial) opposed Mr. Bolton’s nomination in the first place, arguing that at the very minimum, an ambassador to the United Nations should be someone who believed the organization deserved to exist. "

Bolton didn't believe the UN deserved to exist, just that it should exist in the current inefficient, corrupt and utterley ineffective state. After so many scandals, he wanted a positive change at the United Nations.

Perhaps the NY Times is okay with the Secretary General's relatives being paid in an attempt to influence the most senior position in the UN ("Oil for food scandal", which the NY Times failed to put on its front page - ever!). Or perhaps the NY Times is okay with a UN "Human Rights" Council that excluded the USA while such freedom-loving countries like Sudan, Libya, Cuba, etc. run the council.
If the NY Times thinks the United Nations is being run effectively than the NY Times should change its slogan: "All the News That's Fit to Print" to "Hear no evil, see no evil".