I think their popularity was outweighed by the skittishness of some of the PTB, and skittishness won.
In my experience, Luke/Noah were often blamed (unfairly, I think) for the show's falling ratings. They were popular, at least at first, with younger and newer viewers (I'll include myself there - I'd only started watching around the time Luke came out, and only stayed with the show for about a year). But I remember seeing a lot of comments about how long-time viewers were abandoning the show. I find it hard to believe that most of them were actually quitting on a show they'd watched for years because of one storyline, but I guess I can't say for sure. I'm of the opinion that the horrible writing and poorly-done plots in general were a bigger part of the reason, along with all of the other problems that soaps were facing as a genre by then.
In any case, the PTB were never able to create a genuine long-term storyline for Luke/Noah or treat them like any other couple. Instead, they had short-term outlandish stories (Ameera, the Z-twins, etc). Various factions behind the scenes always seemed to be at war about them - what to show, what not to show, etc. People were up in arms over every kiss and every almost-kiss, and the story's speed bumps designed to create drama (and keep them apart) eventually had the unintended effect of making a number of fans dislike Noah. It was a shame, because as a couple they had great chemistry and a lot of potential. Luke was a wonderful legacy character and Van Hansis played him well. Jake Silbermann was a bit less seasoned as an actor though very likable IMO, and I thought he did a good job with Noah. But the writing for them was so bad it was laughable and the PTB support for them was mixed at best.
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