system
Given the following post, respond as if you're commenting on Reddit:
human
[Agents of SHIELD/MCU] Who is paying the SHIELD agents'/researchers'/engineers' salary post-HYDRA?

You could argue that Coulson, May, Fitz, Simmons, and Skye would do it for free, but we also see a fully staffed base throughout season two.

Even if they aren't getting paid, someone still has to pay for their food.
gpt
Reappropriation of Hydra assets goes a long way toward keeping the base running.  
That's why it was tough keeping the bus fueled at first, but as they regrow and gain operational capability, it gets easier.  
In a pinch, there's also merc-work they could do that wouldn't necessarily be mission conflicting.  
Also, Fury's toolbox probably contained information about reserve assets for just such a situation.