Look at some of the biggest stars WWE have created in the past decade, many of them are wrestlers who came from the indies - it's something WWE have used both as a storytelling device (the wrestler from the "minor leagues" trying to prove they have what it takes for the big time) and as an easy way to hype up a new signing by lauding their pre-WWE accomplishments. It shouldn't be surprising that some fans might see pre-WWE experience as a positive, especially if their favourites have include the likes of Punk, Bryan, Seth, Owens & Styles over the past few years.
But this is all an over-simplification, it's disingenuous to imply that a wrestler's background is the major reason fans like or dislike a wrestler. Look at Charlotte, no one trashes her for a lack of ability, no one looks down on the fact that she has never worked a match outside of WWE, mainly because she delivers in the ring. Other's don't. That's not to say they can't play a character, fulfil a role or even win a championship if the story dictates it, but to imply that people don't like them simply because of some misguided idea that they never "paid their dues" is an insult to the intelligence of the majority of the audience.