Rep. Brad Miller, a North Carolina Democrat who is a longtime critic of the big banks’ mortgage lending misdeeds, contends they might be. He wants a top federal regulator, the Federal Housing Finance Agency, to join investors who are trying block the megadeal BofA (BAC) unveiled late last month, according to a letter he sent the FHFA this month.

BofA said June 29 it would pay $8.5 billion to resolve mortgage-repurchase claims filed last fall by major institutional investors including BlackRock and Pimco. Under the deal, Bank of New York Mellon (BK), the trustee for the trusts holding residential mortgage-backed securities issued by BofA’s Countrywide unit, won’t force BofA to repurchase mortgages that failed to meet the bank’s underwriting guidelines.

BofA called the settlement an “important step” in moving past the problems it took on in its 2008 acquisition of Countrywide, the giant subprime lender that nearly collapsed in the early stages of the financial crisis. Investors have feared that the Countrywide deal exposed BofA to massive repurchase costs due to Countrywide’s apparent failure to abide by the so-called representations and warranties in bond offering documents.

Miller, who has been complaining for years about the big U.S. banks’ failure to lend responsibly and about regulators’ failure to rein them in, suggests in the letter that the BofA settlement may be a better deal for BofA than for holders of mortgage-backed securities – including U.S. taxpayers, thanks to the bailouts.

Miller’s July 8 letter to FHFA acting chief Edward DeMarco notes that BofA’s settlement amounts to just 2 cents on the dollar of the bonds’ initial par value and just 5 cents on the dollar of the bonds’ remaining unpaid balance.

That’s not much – and the difference could be coming out of your pocket, Miller contends. He writes that Fannie Mae and Freddie Mac, the government-backed mortgage investors that were bailed out by Treasury in September 2008 and are now overseen by the FHFA, have “suffered substantial losses” on investments in the securities that are subject to the settlement. He didn’t offer any specifics on the losses.

[cnnmoney-video vid=/video/markets/2011/07/06/mkts_midday_bac.cnnmoney/]

Because protecting taxpayers should be the “polar star” of the FHFA, Miller writes, he has urged the agency to “zealously” pursue legal claims against banks that sold mortgage bonds.

An FHFA spokeswoman said the agency has received the letter and will respond to Miller. BofA declined to comment.

A group of bondholders calling itself Walnut Place filed court papers last week claiming the settlement favored big firms with regular business with BofA at the expense of less well connected investors.

Miller makes that case as well, writing that more than 60% of Bank of New York’s trustee business comes from Bank of America.

The notion that taxpayers are footing the bill for BofA’s mortgage problems isn’t a new one either. A mortgage putback settlement the bank reached in January with Fannie and Freddie was received scathingly by critics of the big banks, who argued the administration would do anything to avoid a housing downturn.

Miller stops short of conspiracy theories but contends the government must be more forthcoming about the banks’ response to the housing crisis.

If nothing else, he says, the FHFA should disclose what it knows about Fannie and Freddie’s losses on mortgage securities covered in the settlement — including whether BofA and the Bank of New York have responded fully to subpoenas the agency issued last year to determine whether bond-issuing banks should make good on Fannie-Freddie mortgage-bond losses.

“It is important that the American people know that their government is acting on their behalf, not on behalf of powerful financial institutions,” Miller wrote.