Allowing for paid mods on the Steam Workshop was a bold move, one that could have ushered in a new era of mod making. Change is scary though, and whenever you try to change something people are going to get a bit upset. That's normal though and as time passes and people start seeing what those changes actually mean and they suddenly seem less scary. People were afraid about what they thought paid mods meant however they might have not understood all of the benefits that they may have meant.
There are things that Valve did wrong however which could have
Valve needs to police the paid mods section of the Steam Workshop and keep sub standard mods out of it. Yes this means that Valve has to spend money to curate it however if paid mods do well (like Valve should want them to) then it should pay for itself. At the very worse Valve can appoint community members as mod curators which will weed out mods of poor quality which nobody would buy.
This could even be expanded upon by having certain requirements that paid mods must meet to be sold on the workshop however I'm not going to get into that.
The cut modders get
Core mods going paid
This is a very grey area. I believe that the author of SkyUI should receive monetary compensation if they wish, however since many mods already rely upon SkyUI it would be unfair to force all the players who wish to use those mods to suddenly have to pay for SkyUI. I believe a solution to this would be to make SkyUI free and instead a small percentage of the profits from all the paid mods that rely upon SkyUI will go to SkyUI's creator. This will solve the problem of the creator wanting compensation from their work as well as keeping free mods which rely upon SkyUI free.
Another solution would be to enable developers to release two version of their mods, a free version and a paid version. In this instance SkyUI could have a free version which free mods can depend on, and a paid version that offers more features that other mods can take advantage of if their users have the paid version of SkyUI. This would be a somewhat tricky solution to implement since it would mean that mod makers who depend on SkyUI would have to write code to support whether the player has either the free version or the paid version.
This sort of situation however really only happens when a core mod suddenly goes from free to paid probably wouldn't happen if the ability to sell mods was present at the time the Steam Workshop opened for Skyrim.
There is still potential
Allow mod makers the opportunity to work on their mods full time if they wanted to
Encourage developers to provide better support to their mod communities
More great mods becoming great products, like Dota, Counter-strike, DayZ, and Killing Floor, and we wanted that to happen organically for any mod maker who wanted to take a shot at it.