And now the government has accepted it must do more to convince people of the need for change. It is planning a "listening exercise" which could be fronted by Prime Minister David Cameron and Deputy Prime Minister Nick Clegg.
But what are the points of contention and what wriggle room is there?
Pace of changeThe government has not been hanging around. The bill is still working its way through Parliament, but already 90% of GPs have signed up to the scheme. Many have even started piloting it.
The plan is for the new system to go live in 2013. But there is concern this is being rushed through without proper testing and debate. Some have called for the 2013 deadline to delayed to allow a gradual evolution towards GPs organising local services.
The government has already acknowledged that there may be some GP consortia that will not be ready to assume responsibility for the budget. In that situation, the national board, which will be headed by the current NHS chief executive Sir David Nicholson, will be ready to support the GPs.
Expect more detail on how this "hand-holding" will work in the coming weeks as the government attempts to reassure people.
CompetitionThis is a key area of dispute. The British Medical Association and some Labour MPs have expressed concern that the plans will allow private health firms to get a stronger foothold in the NHS. They already do a little bit of NHS work - about 3.5% of elective operations such as knees and hips.
The critics argue that the bill will allow competition law to be applied to the health service and lead to a much greater involvement, which in turn could undermine local NHS hospitals. The BMA has even likened it to the privatisation of utility industries.
The government has already given some ground on this by promising to make amendments to the bill to stop private companies "cherry-picking" the easiest patients.
This refers to the suggestion that private hospitals only treat patients where there are unlikely to be complications that require longer hospital stays and more complex treatment. The attraction of these patients is that under the NHS payments system they tend to be the most profitable.
However, on its own, that is unlikely to be enough to placate the critics. This could well be the key battleground.
The focus on GPsThere has been some disquiet ever since the plans were first published last summer about the amount of power GPs were being given.
Some doubted whether they had the expertise to take control of the budget, while others claimed there would be substantial conflicts of interest as they could benefit from some of the decisions they take.
The House of Commons' health committee has suggested the government let other experts get involved, including hospital doctors, public health chiefs, social care staff and councillors.
The idea has received some wider support and the government has agreed to give it consideration. Although those close to Health Secretary Andrew Lansley have said he is concerned the consortia could become too unwieldy.
AccountabilityThis is at the technical end of the debate. But for those who work in the health service or try to hold it to account it is a big deal.
The NHS is already secretive when compared to local government which is much more used to holding public meetings. However, the fear is that GP consortia will just make this worse as GPs are effectively private businesses.
Ministers have argued that they will be forced to produce accessible annual accounts and will have to answer freedom of information requests.
But some have argued the government needs to go further and insist they hold regular meetings in public. Again, this is likely to be an area where some ground is given.