Sure, Manchin is relatively popular (hard to tell with so little polling in the state); he would probably be the favorite, but not overwhelmingly so. But this is a year in which the Democrats already have to defend Senate seats in states they never expected — California, Washington, Wisconsin — and so this adds one more battlefront. The DSCC just isn’t going to have enough resources to fight everywhere; Manchin is probably going to be on his own for much of his fight. For what it is worth, Obama is terribly unpopular in the state.
With a Capito-Manchin race, the GOP has at least a decent shot of winning the seat, something they haven’t had in decades of campaigns against Robert Byrd or Jay Rockefeller.