Those that did not trust in the guild and/or just could not afford the join. The joining of the guild might have been free but there were fees and other things that came along with doing so. Merely taking on quests and tasks had some red tape to them that would get in the way of things at times since various parties needed to be compensated for their time and effort.
The Guild maybe have been a part of all government from the shadow but that in turn meant that they could not be funded by them. Even though they were that in reality to the public they were an independent third party that was neutral. So how was a neutral at least on paper group supposed to make the money needed to fund their own operations? The adventurers themselves could not be made to burden the entire cost of keeping the guild afloat so the cost of doing so was spread around to all those involved.