Apparently, missed games have increased 26 percent from 2006 to 2008, and this year is roughly in line with 2008.
To explain this, the NYTimes article sites a number of possible factors, from teams using the DL creatively to expand the 25-man roster, to improved diagnosing technology, but the simplest explanation is that it's harder to play hurt when you're not on drugs. The league began testing for amphetamines in 2006, and it became a major deterrent in 2007 (according to the article).
This obviously has fantasy implications - if it's harder to play through pain and nagging injuries than it was three years ago, players like Aramis Ramirez and Carlos Quentin might have to be discounted.