Correction, Makhno's army did commit antisemitic pogroms, but Makhno himself was not antisemitic as he shot the pogromists and then armed Jewish communities to protect themselves. He didn't do this for Mennonites though. Makhno still has command responsibility for those.
Here's what a comrade wrote in a reply:
it's not true that Makhnovists did not commit antisemitic pogroms. there was at least one well-documented instance: on 12 May 1919, Makhnovists murdered 20 Jewish people in the Gorkaya colony. the case was investigated by the Makhnovist intelligence agent Nikolai Chubenko, who found the Makhnovist unit guilty of committing the pogrom. Nestor Makhno himself then ordered the participants be shot, rather than sending them to the front as was recommended by the investigation commission.
there's also at least a couple other cases: in August 1920, a joint group of Makhnovists and Ukrainian nationalists carried out a pogrom in Shishaki. Makhno again ordered the execution of the people who participated. Makhnovists may have committed antisemitic pogroms in Nechaevka and Kazanka, but the evidence on those is less solid.
Makhno noticed antisemitism among local anarchists and insurgents from the moment he arrived back in Huliaipole in 1917. it was so strong he gave Jewish colonies in the area rifles so they could protect themselves.
Makhno was not personally antisemitic, but that did not extend to many in his army and he constantly had to repress antisemitism.
(Source: Michael Malet's "Nestor Makhno in the Russian Civil War", pages 168-174)