I agree with the others, the GC is trying to take some of your profits.
Your labor rate will have to go up to make up for the lack of profits on the materials. If the GC has any sense, he knows this. He is trying to take your money.
It's a hard decision sometimes. If you are slow, this may look attractive. There has been more than 1 thread about standing your ground, let the job go, no take a job at any profit just to keep working and make something, etc. etc.
There is one forum member that routinely said you have to adjust to the economy and take jobs where the market will price them instead of walking away. After a while, he was asking about what it was like working at the big box stores and what kind of money you could get paid taking a job in electrical maintenance. The point is, taking jobs at reduced rates to keep working can be a losing scenario. But...... you do have to eat.
My recommendation is to have a discussion with the GC. Tell him you understand that the economy is tight and we are all trying to get by. There are costs that he does not see when he supplies the materials. He will probably want you to give him a list of materials, is he willing to pay you for your time to make the list? Since you are not in control of materials, is he willing to pay all lost time if something is missing? How would he feel if a customer said "I want you to build my house, but I'm going to hire all the subs directly and you manage them, plus give me a list of the lumber you need and I'll put it on the job site?
It's not a good path to start down. The GC will probably be able to find someone to play his game, so it's up to you to sell him that although it looks good to him, it's just not the best way. Or, I guess you could be that someone (I would not recommend it).
Good luck.