Can a company use a method published in an academic paper to make money?
Any idea that is in the public domain, is in the public domain and anyone can do what they want with it. The same goes for results. 

Code is a little different, and will be covered by the appropriate copywrite laws, and many pieces of code will have a software licence that has to be adheard to. But thats just the code itself, not the algorithmns implemented in the code. Which are public. 

There is no difference in this regard between open-access and paid-access journals.