(Read more: JPMorgan pays hefty cost for 'Whale', settles for $920 million)
"You never like to see litigation costs, but what happened Thursday doesn't change my expectations of their regulatory exposure. it actually just closes one question from being open," said Jeffery Harte, an analyst at Sandler O'Neill & Partners. "I don't see anything in here that changes my opinion. They're one of the best fundamentally performing banks out there and will continue to be."
Added Harte: "We've got a buy on JPMorgan and this doesn't change it."
So far, JPMorgan's stock price has echoed Harte's positive view. Shares traded slightly lower Thursday, falling about 1.2 percent, but the stock is up more than 20 percent this year despite the bank now facing billions of dollars in legal costs annually (it paid about $5 billion last year, according to its 2012 annual report).
The stock's under performance, analysts say, is in part due to the string of bad headlines for the bank around regulation. Recent troubles include a probe into hiring practices in China; lawsuits over failed credit unions; and an investigation into its energy business.
With all the coming actions, JPMorgan faces a $6.8 billion bill from future legal costs, above the level it has in reserves. CNBC reported this week that Jamie Dimon, JPMorgan's chairman and CEO, told the company's executives that he added 4,000 employees and spent $1 billion more on controls and oversight, with $750 million alone on ongoing government consent orders.
Those regulatory woes have made the bank's stock is relatively cheap, according to analysts.
"We believe if JPM can successfully resolve its regulatory and legal headline risk in a timely manner, the stock could reverse its recent underperformance that has resulted in trading at a below-peer forward (price to earnings ratio) of 8.8 times despite our expectations of above-average profitability in 2014," Matthew Burnell, an analyst at Wells Fargo Securities, wrote in a research note Thursday following the fine.
Analysts at S&P Capital IQ even changed their outlook from "buy" to "strong buy" Thursday, noting that the bank is one step closer to ending its regulatory problems. "We see JPM as one of the most attractively valued U.S.banks," said S&P Capital IQ analyst Erik Oja in a note Thursday. "Over the next year, we expect JPM's forward multiple to rise towards peers as it takes steps to address regulatory actions, strengthen capital, and cut non-interest expenses."
(Read more: As inquiries persist, JPMorgan loses favor with regulators)
Others expressed some concern.
"We expect the stock to be in line with general market performance—nothing better or worse," said Paul Miller, an analyst at FBR Capital Markets. "JPMorgan is a good bank, but it has lots of litigation issues lurking around. What the final price tag is, who knows. Also, they rely on trading revenues to drive earnings, a very volatile line item that is very difficult to predict and analyze."
(Read more: JPMorgan averts CEO/Chair job split, in boost to Dimon)
Regulators naturally crowed.
"At its core, today's case is about transparency and accountability, and JPMorgan's admissions are a key component in that message," George Canellos, co-director of the SEC's enforcement division, said in a statement. "While not every case will be appropriate for admissions of wrongdoing, the SEC required JPMorgan to admit the facts in the SEC's order—and acknowledge that it broke the law—because JPMorgan's egregious breakdowns in controls and governance put its millions of shareholders at risk and resulted in inaccurate public filings."
Politicians also gloated over the fines, and hinted more penalties were in order.
"The size of the penalties is testimony to the great damage risky derivatives bets can do, and that's important," said Sen. Carl Levin, a Michigan Democrat who helped conduct an investigation into the London Whale trade as chairman of the Senate Permanent Subcommittee on Investigations, said in a statement.
"However, the whole issue of misinforming investors and the public is conspicuously absent from the SEC findings and settlement. Our PSI investigation showed that senior bank executives made a series of inaccurate statements that misinformed investors and the public as the London Whale disaster unfolded.
"Other civil and criminal proceedings apart from this settlement are continuing, so there is still time to determine any accountability on that matter."
Rep. Maxine Waters, a California Democrat, was pleased.
"Today's announcement of fines levied against JP Morgan validates Congress' decision to provide our regulators with broad authority to regulate derivatives trading whenever it affects the U.S. economy, including overseas," Waters said in a statement. "These actions, as well as those expected by the CFTC, send a powerful message to Wall Street that when it engages in irresponsible behavior, it will be held accountable."
Some lawyers were underwhelmed by the fine.
"The internal controls and supervision failed miserably at JP Morgan," said Chicago investment fraud attorney Andrew Stoltmann. "Instead of senior executives being forced out or even criminally sanctioned, the firm receives a fine that amounts to little more than a slap on the wrist."
JPMorgan, which has assets of $2.4 trillion worldwide, was eager to move on.
"We have accepted responsibility and acknowledged our mistakes from the start, and we have learned from them and worked to fix them," Dimon said in a statement. "We will continue to strive towards being considered the best bank—across all measures—not only by our shareholders and customers, but also by our regulators. Since these losses occurred, we have made numerous changes that have made us a stronger, smarter, better company."
—By CNBC's Lawrence Delevingne. Follow him on Twitter @ldelevingne.