I suspect that people have a negative perception of Southwest Airlines for one or more of the following reasons:
None of the above for me. Southwest doesn't offer redeye flights, doesn't offer assigned seating, doesn't fly to several major airports/cities, and doesn't fly internationally, which to me translates into wasted time-- wasted daylight in an aluminum tube; wasted time in line or trying to check in at midnight from a cell phone; wasted time getting to Manhattan from ISP/Beacon Hill from MHT/West Seattle from... PDX; wasted time flying miles I could have banked towards New Zealand or India.
And perhaps more to the point, for the routes I fly, it's not that cheap. While not as expensive as Jetblue, I've found BWI-xxx-SNA consistently to be the same or even more expensive than on United at the times I want to fly-- Southwest had nothing under $400 this year.