Companies provide another level of information about users. When you create a user you can assign the user to a specific company.
Companies are not compulsory in the knowledgebase. You would use them if your users were from a small number of companies, but if your users came from all around the world and were a mix of individuals and company users you probably would not bother.
Some examples where you might user them:
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Your users come from a finite number of companies and you have multiple users in each company
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When you license the knowledge in your knowledgebase and charge the company for access
Some examples where you probably wouldn't:
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Your users come from all around the world
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You would have to set up a different company for every user
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When there is only one company (although you could also set up the company in this case; it wouldn't matter either way).