Of course Walt loves Jesse, he never says it but he treats Jesse sort of as the son he "never had" because Jesse can participate fully in the part of his live he loves while Jr. cannot. That's why he fights to keep him alive in S3 when Gus would have him killed. He didn't kill Jane primarily to manipulate/hurt Jesse, it was firstly because she was dangerous and unstable and threatened to ruin Walt's life of crime, and secondly because she was very bad for Jesse(turned him into a heroin addict, remember?)
One of Walt's characteristics is his pragmatism which is what drives him to do normally unconscionable things like having Jesse murder Gale or poisoning Brock. He does the things he thinks he needs to do in order to stay alive, or to stay ahead of his enemies, or both. ---