I get the feeling that Brahma sees Kubera as a rebellious son. He survived the previous universe without siding with Kali, so he's one of the few creations she considers to be truly successful. So despite him opposing her current goals, she likely wants him to survive the destruction of the current universe and move on to the next one. Indra, on the other hand, is probably desperate to prove his worth to Brahma so she'll let him move on to the next universe as well.
