FORTUNE — Jack Lew, the frontrunner to be named Treasury Secretary in Obama’s second term, isn’t Wall Street’s first choice for the key economic post. He’s not even its second.

“I’ve talked to a bunch of investors and it’s seen as a net negative going from [Tim] Geithner to Lew,” says Chris Krueger, senior political analyst at Guggenheim Partners. “Who does Wall Street want? Not Jack Lew.”

Lew, 57, spent three years on Wall Street working at Citigroup (C) as the chief operating officer of its alternative asset investment management unit. One of the funds Lew’s group invested in was run by John Paulson, who at the time was betting heavily against the housing markets and banks. But that’s not the part of Lew’s resume that anyone seems to remember. And it’s certainly not the important part.

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After Lew, a Queens, New York native, graduated from Harvard University and Georgetown Law, he headed straight to Washington and has mostly stuck inside the Beltway ever since. He’s been on teams credited with brokering major budget deals. He worked for Tip O’Neill when the House speaker struck a deal to raise taxes and cut benefits with President Reagan. And Lew was a key member of President Clinton’s budget team, which simultaneously erased the deficit and struck a long-term deal with Republicans to preserve entitlements.

Under Obama, Lew served as the head of the Office of Budget and Management, and at the beginning of 2012 he became Obama’s chief of staff.

Since the election Obama has seemingly been trying to patch things up with Wall Street, which threw its collective support behind Romney. After the election, Obama called JPMorgan Chase (JPM) CEO Jamie Dimon and other business leaders. And Lew recently met with Dimon to talk about the fiscal cliff. Geithner is expected to exit the Treasury job early next year.

Nonetheless, some financial executives say that if Obama were to choose Lew for Treasury Secretary, it would signal that the president is not as serious about mending his relationship with corporate leaders as he says. Wall Streeters say the two other candidates who are considered in the mix for the job, former investment banker and former Clinton White house chief of staff Erskine Bowles and BlackRock (BLK) CEO Larry Fink, would be preferable to Lew. Bowles has been a deficit hawk, and Fink clearly knows the debt market. What’s more, unlike Lew, neither one would need an introduction to Wall Street.

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Don Marron, a dean of Wall Street who was also once rumored to be a top pick for the Treasury Secretary job (under a Bob Dole presidency in 1996), says he doesn’t know Lew, or where he stands on business issues. And Marron says that will be a problem for corporate America and the market. “Lew will be more of an unknown at a time when you don’t want unknown,” he says.

Strangely enough, Democrats don’t seem so excited about Lew either. They don’t think he will be tough enough on Wall Street. And by picking Lew, who has little background in regulating financial markets, Obama would signal that he is more focused right now on striking a budget deal, and less focused on further tinkering with the rules on Wall Street.

Lew wouldn’t be the first Treasury Secretary to come from more of a political background instead of Wall Street or corporate America. James Baker, for instance, served as the Treasury Secretary during Reagan’s second term. But the relationship between the Treasury Secretary and Wall Street matters more than it used to. One of the legacies of Tim Geithner, who is a lifetime regulator, has been to focus the position more on market regulation. The Treasury Secretary is now the head of the Financial Stability Oversight Council, the newly formed team of regulators that is supposed to be on the lookout for risks that could cause future crises. And the relationship between the economy and the market’s performance is much closer than it was back in Baker’s day.

So some of this can be dismissed as more Masters of the Universe griping they are not being heard by Obama. But not all of it.