That was at the beginning of Doomsday Clock, we have no idea what they'll be like at the end of Geoff's story. Clark losing hope can't exactly happen if either the world trusts him above all other heroes or that Lois is fine. According to Manhattan's vision, Clark loses everything that makes him hopeful. That obviously means something happens to Lois as well as the world.
All I'm suggesting is Bendis is possibly making things darker and more dramatic for Lois and Clark so readers aren't taken completely by surprise when something happens to them in Doomsday Clock.