Popeye Muttered Because He was Animated Prior to Being Voiced
The real reason Popeye murmured under his breath is quite straightforward. The animation and voice acting fell short of expectations. The old salty sailor appears to be speaking, but his lips aren't moving, giving the idea that he may be speaking under his breath because the animation was completed before the voice acting was added.
Today's cartoons probably wouldn't get away with this, mainly because the viewers could perceive it as laziness and the effect would be lost on those who have grown up with CGI getting better every year. Even so, there might be a valid explanation for why Popeye hasn't made a comeback. It's possible that his many different mutterings would be challenging to animate or even impossible to replicate because whoever did it would have to at the very least research Jack Mercer's dialogue from the original cartoons to make it sound somewhat genuine.
However, the idea of Popeye might be out of date because, if you recall, he wasn't the most politically correct character ever. Bluto was significantly worse, but he wasn't the worst by a by shot. However, animators don't seem to go for a fist-based approach unless their subjects are inherently physical in nature and are intended more for older children who can distinguish between truth and imagination. You could argue that Popeye was targeted at the same age group, but at this point, at least in kid cartoons, the idea of eating spinach to become a tough guy and then just clobbering the bad guy isn't something that people want to see.