There were 45 no votes on the clean continuing resolutions. That’s enough to block funding of the government. A majority is not sufficient.

Yes, the republicans hold a majority in the Senate, but the Senate rules require 60 votes to stop debate on a bill (ie cloture). So, the Democratic members are holding up the CR by not voting for cloture.

Cloture is a very valuable tool for the minority in the Senate to keep the majority in check. Cloture is just a rule which can be changed by just a majority vote. I think it's a mistake for either party to do away with this rule. For example, during the Obama Administration, the Democratic members of the Senate changed the rules to allow federal judges to be approved with just majority vote. Then, during the first Trump Administration, the Republican members changed the rules to include supreme court judges, which lead to the current supreme court.