If you can handle the flight times (and that's a big if for many people) there is absolutely nothing wrong with flying Copa to SCL. I've even done it in coach, and it's generally no more uncomfortable than travelling in coach on a larger aircraft. And Copa has decent service, even in coach. And, as others have noted, transiting PTY is no big deal whatsoever. They even have a nice President's Club lounge.

BTW, with CAL starting its own nonstop service to EZE from IAH, have you considered making a connection in EZE? Don't know about the SCL-EZE fares these days, but I presume they're not outrageous.