Yes, only a small amount of the money goes to the troop. The lion's share goes to the scout council, and that's not as bad a thing as it sounds:
The scout council supports camps, which the troops can use for a token fee. Troops can camp for only $25 or so a weekend, and when they use Girl Scout camps, the leaders can feel safe knowing that they're not camping next to a group of unknown people in a public spot.
The scout council provides loads and loads of programs that the troops can attend at low cost -- programs that all troop leaders don't have resources to provide. For example, years ago my girls did an overnight at a history museum, behind-the-scenes trips to the baseball park, indoor rope climbing. Oh, and science workshops at the council office for $2/girl.
However, the last few years my girls were involved, they were "over" cookies. The little girls get very excited about cookies, but later . . . not so much. I did start writing a check directly to my girls' troops, saying that this is NOT connected to cookies; if it's connected to cookies, the troop leader is supposed to share with the council office. Rather, I said specifically, "This is a direct donation to the troop, to be used by the girls in this troop." At the point my girls "outgrew" cookies, they also "outgrew" most of the council's programs, so I didn't feel badly about supporting JUST our troop.