A lot of this hit the fan about 10 years ago when a crash was partially blamed on the pilot working two jobs, being overtired and overstressed, and then crashing with a load of passengers. People were shocked at an airline pilot would have trouble feeding himself on just one job. I don't think much has changed since then.
There have been changes. Standards for pilots of the tiny airlines have been raised a bit, extra restrictions were put on their schedules, and loopholes that allowed reducing pilot pay have been closed.
But most importantly, the big airlines are now held responsible for those tiny regional/commuter airlines they're contracting with. The big guys no longer get to take your money and book you on a tiny turboprop (with their logo on the side) while washing their hands of the poor safety record of those "regional" airlines. Their own big pockets will be the target of any future lawsuits.
However, the practice has continued:
"A government study recently found 61% of all advertised flights for American, Delta, United and US Airways (now merging with American) were operated by regionals in 2011, up from 40% in 2000." http://www.usatoday.com/story/...
If you're smart, you avoid regional airlines. The accident rates are dramatically higher, and you're saving little, if any, money booking flights on them.