Since when was air travel "public transportation"? Which government agency owns and operates Southwest Airlines? Heh, we have this jaded notion that flying is public transport because we've all been so f*cking willing to hand over our rights in exchange for some illusion of safety. News flash...just because the *****ebags of Homeland Stupidity set up shop at the gates with their guns and x-ray vision doesn't mean that Southwest Airlines is "public transportation".
Secondly, as EdWort notes above, regardless of how much effort the parents made to control the kids, the fact is that they were making a mess of the plane, running around when the fasten seatbelt light was on (dangerous not only to them but to others), and creating a chaotic environment. Regardless of their disabilities, regardless of whether the parents get an "A for effort", the reality was that they were creating a disruptive and possibly dangerous atmosphere and the airline should be able to maintain discretion in such cases. There are other methods of travel, and if their disabilities really were that uncontrollable, then it's necessarily the case that the parents were irresponsible for hauling them onto a plane in the first place. There are always other options, including tranq drugs like Ed noted above.