Because if a Democrat wins in 2020 but the Senate is still finely balanced, Manchin is still a likelier vote for Democrats than even the most "moderate" of GOPers like Collins. And the Republican that takes over from Manchin in Trump-loving West Virginia would take that seat, hold it for multiple cycles and be as anti-Dem as someone could possibly be.
See this from 538 last year -
https://fivethirtyeight.com/features/liberals-would-be-foolish-to-target-joe-manchin/
By all means primary the guy, but he's literally just had one, against a progressive, and won it by 40 points. In a situation as shitty as the US Senate is for Dems, how picky can you be?