I haven't ever worked for either airline, but I've worked plenty around both.
What's the difference? Mesa pilots get screwed, even with a union. Skywest pilots seem pretty happy, and don't feel that giving 2% of their income to ALPA will make life any better for them.
Seems like most of the Skywest bashing comes from people who either didn't get hired or lost business to them.
Heck, the main common ground between Skywest and Mesa, their costs are low (or were, in the case of Mesa), and they are (or were) able to underbid others in the industry. It pi$$es people off, and then they come on to FI, calling Skywest "scabs" and all other kinds of names. There's a lot of Mesa bashing too, but much of that is actually coming from current and former Mesa pilots (that, and there is a much more factual base for the bashing, such as the "campouts").
Most Skywest bashers have an agenda. If Skywest were to unionize, it would level the playing field for other airlines. I wouldn't be opposed to this personally, but why should we pressure them to "give up" what is percieved to be the "upper hand?" If they're happy, let them be. If they're not, they can vote in a union or get another job.
Skywest isn't perfect, sure, I have mixed feelings about them (particularly when they go calling themselves a "major airline"), but I don't think they deserve near the controversy people try to strike up about them.