Boy, does this have a bad smell – which, I have a feeling, will only get worse the longer it sits out in the sun. 
Since this is a long article, I thought I’d drop some highlights here.
In the three years after he arrived in Washington in 2014, Matthew G. Whitaker received more than $1.2 million as the leader of a charity that reported having no other employees…
The Foundation for Accountability and Civic Trust described itself as a new watchdog nonprofit dedicated to exposing unethical conduct by public officials…
So at the same time that Whitaker was being paid by this “charity” as a “watchdog … exposing unethical conduct,” he was also being paid by an unethical company that bilked its customers out of millions of dollars. 
Contrary to its claims in news releases and a tax filing, the group was created under a different name two years before Whitaker’s arrival, according to incorporation and IRS records…
In its application to the IRS for status as a tax-exempt organization, the organizers reported that the group would study the impact of environmental regulations on businesses, records show. In that incarnation, the group took no action and “only existed on paper,” one man named in IRS filings as a board member told The Washington Post. Another named in a state filing as a board member said he never agreed to be on the board…
Whitaker’s 2017 pay from the charity — more than $500,000 for the first nine months, or half the charity’s receipts for the year, according to tax filings — and the group’s earlier, dormant incarnation have not been previously reported by media…
James Crumley, who provides marketing services to conservative nonprofits and campaigns, was listed in an IRS filing as one of the directors. In a phone call, he initially said he did not remember anything about the group, including why it was formed.
“I can only speculate since I didn’t even remember this group existed,” he wrote in an email later.
Crumley said he’d learned that the group held no meetings and apparently had no bank account in its first two years. “The organization only existed on paper and didn’t do anything at all,” he wrote.
Looks like you could call this a “charity shell company” and that’s not suspicious at all. 
Noah Wall, now a vice president of advocacy for a conservative nonprofit called FreedomWorks, was listed in Virginia state filings as a director of the group in 2014. Wall said he was surprised to learn of his role. He said he was approached by Wotring but never agreed to join.
“I never signed anything,” he said. “I’m not entirely sure what any of this is.”…
Yes, everything’s completely above board here.
On July 21, 2014, the IRS approved the group’s application for tax-exempt charity status…
The next few paragraphs describe how the “charity” kept changing its name and purported mission while changing its address from a UPS drop box to a “virtual office and mailing address shared by 200 organizations.”
“It’s very possible that this organization is misusing its status as a charity,” said David Nelson, a specialist on nonprofit organizations and a former tax partner at the Ernst & Young accounting firm, who reviewed the group’s tax filings at The Post’s request. “It appears the IRS never gave approval to FACT.” [The Foundation for Accountability and Civic Trust is the most recent incarnation of the charity and the one which paid Whitaker.]
In its federal tax filing for 2014, FACT declared that it had not changed its name or its mission that year, records show, and there was no mention of the prior names. The spokesman for FACT declined to provide documents that he said showed it had notified the IRS of the name change.
In the 2014 filing, FACT reported that it had no employees and that it paid Whitaker $63,000 for three months of work, 30 hours a week, as president and director…
The remainder of the article includes some excellent research work by the WaPo establishing that, despite FACT’s claimed “nonpartisan” mission, it was indeed highly partisan. This would appear to disqualify it from tax-exempt status (my conclusion, not the WaPo’s).
The WaPo also attempts to trace the funding for this “charity,” and makes some headway, but just like Manafort’s shell companies, the funding was routed through multiple layers of various financial entities, making the ultimate source virtually impossible for a news organization to trace – perhaps a congressional committee with subpoena power could uncover the true source (again, my words, not the WaPo’s).
The article concludes with a tally of Whitaker’s take.
In the three years he worked at the charity, Whitaker’s pay rose sharply each year, tax filings show. Last year, he was paid $55,000 a month. In all, he earned $1,219,000 — more than a third of the donations the group received from 2014 to 2017. 
