Sort of like a paid vacation--you were there, on orders, ostensibly, to do work, but in reality you were goofing off and partying. For example, weekend trips to Cubi Point, PI were generally considered to be boondoggles.
This civilian explanation of the word does not convey the full military meaning of the term;
boon·dog·gle (bndôgl, -dgl) Informal
n.
1. An unnecessary or wasteful project or activity.
2.
a. A braided leather cord worn as a decoration especially by Boy Scouts.
b. A cord of braided leather, fabric, or plastic strips made by a child as a project to keep busy.
intr.v. boon·dog·gled, boon·dog·gling, boon·dog·gles
To waste time or money on a boondoggle.
http://www.thefreedictionary.com/boondoggle Afghanistan is not a "boondoggle." Those servicemembers who are there aren't partying, discoing, or going on shopping sprees. They're targets for Taleban bombs.
It's not a good word to use in the context that you wish to use it. If you want to say that the Afghan war is a money pit, say that. It's not a boondoggle, though.