It's an old joke amongst journalists that the role of the press is to "comfort the afflicted, and afflict the comfortable." Ben, I think this piece is fair, and the reporter obviously takes pains to describe the trip exactly as he saw and experienced it. Once an organization becomes the behemoth size that charity: water has, it demands a higher degree of scrutiny because of the sheer number of public donors who want to make sure their donations are well spent.
The article actually steers clear of some of the more weighty concerns out there (see for example this oft-cited piece: http://truth-out.org/opinion/item/13814-the-problem-with-charity-water) about partnerships with organizations like Samaritan's Purse, whose express mission is to gain an audience for Christian gospel through the provision of food, water, and medical assistance (http://www.samaritanspurse.org/our-ministry/about-us/). That makes some people uneasy.
Needless to say, charity: water is obviously a powerhouse in fundraising, PR work and awareness, and does tap partner organizations working on the ground already. Not a bad partnership model for other aid organizations to consider, even if it's not perfect.