is pretty clear when you realize that only 4.3%[0] of their profit is for charities that they _only stand for money_, they use the rest for privately own businesses (incl. hospitals and schools, but completely private and run like businesses)
They also (currently, not in the past) been linked with money-laundering [1]; by the way your premise of the organization being decentralized and consequently non-responsible for the doings of their members is false; specially when they have special access to far more financial secrecy than the average bank or person.
Plus they are still a great spot for pedophiles[2] to do their things, even with the current pope they do not accept their bad handling of the acussations [3]
[0]http://www.patheos.com/blogs/friendlyatheist/2012/08/17/the-...
[1]http://www.bbc.com/news/world-europe-25831234
[2]http://america.aljazeera.com/opinions/2014/2/the-vatican-sti...
[3]http://www.huffingtonpost.com/2014/03/05/pope-on-pedophile-p...