This is problematic because it's no longer obvious that a user belongs
to a particular company.
Sometimes this may highlight a problem with your domain model. Why does a user belong to a company? If I change companies, am I whole new person? What if I work for two companies? Am I two different people?
If the answer is yes, then why not take some company-unique identifier to access a user?
e.g. username:
company/foo/user/bar
(where bar is my username that is unique within that specific company namespace)
If the answer is no, then why am I not a user (person) by myself, and the company/users collection merely points to me: (note: employee seems to be more appropriate)
Now outside of your specific example, I think that resource-subresource relationships are more appropriate when it comes to use rather than ownership (and that's why you're struggling with the redundancy of identifying a company for a user that implicitly identifies a company).
What I mean by this is that users is actually a sub-resource of a company resource, because the use is to define the relationship between a company and its employees - another way of saying that is: you have to define a company before you can start hiring employees. Likewise, a user (person) has to be defined (born) before you can recruit them.