Two things I would say, though I am an atheist without having been a Catholic I have a degree in theology from a Catholic University: 
 The first is the emphasis on hierarchy "we believe such and such not so much because the bible says it is so but because it is tradition and approved by popes as apostolic successors and the vicar of Christ."  I think this is really the dominant reason, people looking to discern the will of god for their lives become a bit disheartened when they realize just how much politics and hypocrisy come along with being Catholic.  
The second reason, the one that applies more to academics is that Catholicism despite its disdain for modernity has in fact been a little more willing to approach science than say a fundamentalist tradition.  In doing so they have kind of let atheism in the back door.  By discussing science on science's terms and trying to cultivate a natural theology which supports revelation they have created a "god of the gaps" type situation that just keeps getting smaller and smaller.  This coincidentally leads to a bigger and bigger dependance on the first problem: the hierarchical dogmatism which becomes less and less satisfying but they more than any others realize that biblical revelation came at a specific time and a specific place and while it is all the word of God it is not all relevant to the same degree...the CAtholic must be looking at the world "the first revelation" to be determining the will of god and weighing this against apostolic tradition.  I think dissapointed catholics realize that this is pretty much what atheists do..just without the God part.  
I am not saying that Catholics are really doing anything wrong, it seems to work for lots of people...and it does build a community that is very strong.
		
		
	 
I would add to that.  It has to do with both points 1 and 2.  
1) causes people to look more at the origins of the tradition, and in the process we learn that a lot of it has to do with superstition, or it is reacting to a culture which is very different than our own.  You don't just learn "scripture" you learn the history and the culture that is also behind the "scripture" and in the process, wonder if its God writing the "scripture" or it is man reacting to a culture he likes/dislikes and then attributes it to god.  A lot of protestant faiths on the other hand are more "mystical" people accept it because the bible says so, without researching the bible itself.
2) Besides embracing science the church has also embrached archelogy and similar fields to learn more about the bible and the vast amount of cultures the 50+ books of the bible are written about.  Archeology has disproven some aspects of the bible/interpretations of the bible (such as the flood, much of genesis, and much of exodus).  This point fuels the other two points by creating doubt.
------------------------------------
The final point I would add to this is the Catholic belief of "doubt," certain things according to the church can't be explained, they know this.  God is beyond our comprehension he is infinite, we don't need to understand the trinity god is one and three, Jesus is in every holy communion.  The philosophy of doubt+the embracing of science and archeology has allowed critical thinking to thrive.  The catholic view of doubt is supposed to stop such critical thinking, but in reality it probably does the opposite.
Spensend2 also makes some good points
------------------------------------
One last thing, Catholicism preaches the hiearchy style of belief, while Protestantism preaches a personal connection with God.  Rejecting the idea of a hiearchy is alot easier than rejecting yourself, even if you aren't rejecting yourself, if that makes sense.