After S.H.I.E.L.D. has been compromised by Hydra, it went dark without any government support.
How was the agency funded then to pay their highly trained staff, contractors, bills, airplanes (e.g. helicarrier) and high-tech tools? This sounds like some unlimited funding.
To quote the new director of S.H.I.E.L.D., Jeffrey Mace to Phil Coulson in S04E02 (14min):
But what I don't have is the anonymous, unlimited funding you seemed to have before. To build billion-dollar airplanes?
What source was he referring to?