In Marvel's Cinematic Universe, S.H.I.E.L.D. has been doomed. Top level agents are either dead, arrested or living in exile. S.H.I.E.L.D. has been labelled as Terrorist Organization. So, previous funds should be gone.
But yet, S.H.I.E.L.D. is non-officially running. Who is funding them? Salary for Agents and fuel for Airplane should be expensive. While Maria Hill is going to join Stark Industries, I don't think Stark Industries would take trouble funding a Terrorist Organization which is non-profitable.