The public currently sees bankers and their bonuses through a red mist. Punches are being thrown, like one-off windfall taxes on profits or bonuses, which may feel satisfying but don't connect with the underlying problems. These relate to having a banking system where profit – and bonus – maximisation occurs on the back of state guarantees, for institutions that are deemed too big or important to fail. As long as the guarantees exist, the key issue becomes one of how best to make banks pay a fair fee for the privileges they enjoy.

The anger has had several causes. Even before the crisis, customers resented the capricious and unreasonable charges, the incompetence and the impersonal nature of modern retail banking. Then, highly paid whizz kids managed to destroy their industry through recklessness – the taxpayer then being called upon to rescue them. Then we had rewards for failure (Sir Fred). And latterly there have been bonuses in institutions on state life support. It is like a building contractor who made a fortune putting up unsafe dwellings and, when they collapsed, made another fortune clearing up the debris.

Of course people are angry, and they have every right to be, especially when so many are losing their jobs in a recession triggered by a banking collapse. There are, however, different types of banks. Bonuses are a big issue in investment banks from proprietary trading, but are rare in retail banks. Some banks over-reached themselves and have been nationalised or semi-nationalised, but others have continued to operate successfully and sensibly – like HSBC, Clydesdale, Nationwide, and the Co-op.

The immediate political question is what to do about bonuses. There will be a crescendo of indignation as bank profits and bonuses are announced in coming months. There is some force in the argument that governments should act collectively through the G20 or the EU, since the bits of banking that generate the biggest bonuses are global. But this can be a cop-out, like those pious calls for "general and complete disarmament" which signal an unwillingness to do anything much about reduction. A policy of unilateral bonus disarmament is less risky, not least because other governments are already decommissioning.

One option is to use nationalised and semi-nationalised banks to set a standard of behaviour, stopping or restricting bonuses. Some of us thought such an agreement was reached a year ago by the government for RBS and Lloyds, but it does not appear to have been implemented. One obstacle is that bonuses will simply be consolidated into basic pay; another that it puts nationalised banks at a competitive disadvantage. The latter could be minimised if government procurement from the banking sector were conditional on a code of conduct neutralising the bonus culture.

Transparency is a good principle, shining a light into dark corners. One investment bank is said to have included cleaners in its bonus head count (without having paid any a bonus) to make payments appear less greedy. Transparency demands that all highly paid staff – earning, say, more than the PM – should declare all salary and entitlements as board directors currently do.

Personal taxation is the obvious way of ensuring bonuses are shared with the public. The top rate of 40% will become 50% next year. But bankers are scarcely trembling in their boots, since the government has left them easy tax-avoidance opportunities. The most glaring is capital gains at 18% – so any bonus paid in shares will attract much lower tax rates on any rise in share price (given current depressed prices, it's a one-way bet).

I am also sceptical about the value of paying bonuses in shares redeemable after several years, an idea adopted by the G20 and now being represented as an original thought by George Osborne. It is a sensible way to discourage excessive risk-taking, and should be pursued for that reason. But free shares in RBS and Lloyds come at taxpayers' expense, and it does nothing to deal with the inequity of excessive rewards on the back of state guarantees. It merely means the next Ferrari is bought on account, rather than with a case of cash. Greed deferred, rather than cancelled.

Another approach is indirect: taxing the profits of banks, rather than the bankers. The demand for a windfall tax reflects the belief that banks should repay some of the money they are earning thanks to the taxpayers' rescue. The rough justice has undoubted appeal. But it risks unintended consequences. Banks are being encouraged by the government to increase profits to strengthen their capital base against future bad loans, and to put the nationalised banks in a better position to repay the taxpayer. A one-off tax will merely postpone this process. It will also encourage the banks to widen their spreads further, hitting job-creating smaller businesses being throttled by extortionate fees and hitting pensioners getting a poor return on their deposits.

Moreover, the underlying problem of state guarantees is not dealt with by a one-off tax. It will continue until the structure of banking is reformed.

A central element in that reform is resolving the "too big to fail" problem highlighted recently by the governor of the Bank of England: UK-based global banks that pile up massive commitments, as well as profits and bonuses, from speculative proprietary trading, all on the back of a taxpayer guarantee. Various ideas are being tossed around to deal with this, but nothing is happening. Meanwhile banks that benefit from a state guarantee should pay for it through a government guarantee fee. Banks are already required to pay to guarantee their depositors, but they are being given free guarantees on the counterparty risk in their "casino activities". The guarantee fee could be paid for through a supplementary rate of corporation tax, or be based on the turnover. It isn't sensible to be dogmatic about means; the key is to have the principle accepted.

Such a considered approach is perhaps less emotionally satisfying than a high-profile penalty on banks or bonuses. I suspect anything short of hanging will not meet public expectations. But bashing bankers detracts from the issue at the heart of the banking crisis: the continuing, dangerous but – usually – profitable behaviour that enjoys implicit protection from the taxpayer. That protection is free for the banks and potentially ruinous for the rest of us. They should pay a proper price for it.