Consumers may feel vindicated by President Obama s new proposal to tax large banks with a new fee.

The fee is designed to recoup the government s losses from the Troubled Asset Relief Program, which has come under fire for propping up financial institutions at the cost of the taxpayer.

But the new fee may ultimately stick the affected banks customers with higher charges, lower yields of deposit accounts and ever-tighter lending standards. The subjects of those fees will try to pass along the costs to their customers," says Jeff Miron, an economics professor at Harvard University. It s not a substantial cause of concern, but it s certainly a cause of concern.

Here s what consumers should know.

Who will have to pay the new fee? The fee will apply only to firms with over $50 billion in assets. About 50 companies will be affected, including the nation s largest banks, thrifts and insurance firms. Small and community bank customers need not worry: These institutions will not be affected. Also spared from the fee are the U.S. auto makers and mortgage companies Fannie Mae (FNM) and Freddie Mac (FRE), even though they are TARP fund recipients. However, American International Group (AIG) will not be exempt.

How much will these institutions have to pay? The fee will equal 15 basis points, or 0.15 percentage points, of a bank s covered liabilities. But any assets held in FDIC-insured deposit accounts will not be included in that calculation. That will ensure the government is not double-dipping; banks already pay an insurance fee to the Federal Deposit Insurance Corporation, says Greg McBride, senior financial analyst at Bankrate.com. It s also more than a subtle encouragement for banks to move away from riskier activity and go back to the nuts and bolts of banking, he says. The government is expecting to raise $90 billion over 10 years and will continue charging the fee until all TARP dollars are repaid.

What does that mean for bank customers? Broadly speaking, there are two possible results. On the plus side, the fee may cause the affected banks to place more of an emphasis on consumer deposits and become more competitive with their product offerings, McBride says. The more assets the bank holds in the form of FDIC-insured deposits, the less it will have to pay of the new fee.

On the other hand, taking money from the banks coffers means these institutions will have less money on hand to lend or to hold as capital against lending. And once interest rates start going up, the banks may not in a hurry to follow with higher yields on deposit accounts. The money flowing out of the bank has a detrimental impact not only on credit availability but also on the willingness to increase deposit payouts even once interest rates start going up, McBride says.

That said, Miron expects the impact to be small because that tax is relatively light. $90 billion to be collected over 10 years spread among the banks is a small tax, he says.

Consumers can t say the same thing for the fees their banks have been collecting from them. Bank fees have been on a steady upward march for more than a decade and the addition of this tax is not going to derail them, it will only add more fuel to the fire, McBride says.