As an example the Taliban was targeting NGOs in the Afghanistan/Pakistan region because they believed efforts to vaccinate against polio were in fact an attempt to poison Muslims. Dozens of doctors, nurses, and volunteers were killed because someone like you decided to start a baseless rumor.
Most first world intelligence agencies have policies against embedding spies in aid operations. When it became common knowledge we used a vaccination campaign to collect on UBL, many people resigned from the Agency.
I wrote about one aspect of that specific case here:
https://medium.com/@roryireland/latest-wikileaks-documents-i...
Or more likely a terrorist organization in those countries started such rumors to turn public sentiment against the west. Oh, and then the USG used a vaccination program to attempt to track down terrorists, which played a role in the take-down of Osama Bin Laden.
It's fair to say that there are compromised NGOs, based on the OBL incident alone.
It really depends on many factors - location, group activities, training, personal, the threats they pose to the actors with the will/desire etc to target them, also how you define compromised (a cleaner keeping tabs? a phishing email opened? a disgruntled volunteer? a paid staff member who walks out the door with data? a leader who has been turned?)
This is actually my gripe with the Dutch pirate party. They are often very alarmist and exaggerate problems in the same way the parties they oppose do. I wish there was a party that's focuses on major issues in stead of exaggerating a small number of issues in order to get popular with a specific market.
I admit I might still vote for them anyway if I can't find a party that better represents me. Fortunately we get quite a few to choose from! Dutch might want to take a moment and be thankful we have that :)