Frank and Lonette's relationship is ultimately very sweet—even though he's a human and she's technically a cartoon character, they really do genuinely love each other. And while the Can't Have Sex, Ever obviously puts a bit of a strain on their relationship, it's ultimately for not just the safety of Frank and the safety of both the Real World and Cool World, but for Lonette as well.
Also, as Frank's preparing to leave Cool World for the Real World to defeat Holli Would and her cronies, Lonette admits that she's against Frank leaving not because she doesn't want him ultimately save both the Real World and Cool World—she's worried that he'll want to stay in his original human world and that she'll never see him again. However, Frank assures Lonette that he really does love her and that, no matter what happens, he will return to Cool World so they can be together.
Though Frank is killed by Holli Would in the process of saving both the Real World and Cool World, he ends up being reborn as a Doodle since Holli was in her Doodle-form when she killed Frank, which means that not only can he and Lonette continue their relationship, they're finally able to consummate it after being together for so long.
Just before they're about to have sex, Lonette questions Frank if he ever considered staying in the Real World so he'd be able to do all the stuff he wasn't able to do in Cool World—Frank tells her that it doesn't matter at this point, since he and Lonette can continue their relationship (especially now that he's a Doodle instead of a Noid).