Companies obtain money and power. Companies use money and power to secure their position, because "make the best product" is usually not the best investment whenever "prevent competitors from reaching the market" is on the table, and regulation is one of the popular ways to achieve the latter.
I think you are confusing the possibility being present with the possibility being realized. In a free market, that possibility is present but unrealized. The possibility doesn't make the market non-free (and anything that would prevent such possibility would make the market strictly speaking non-free), but when entities choose to act on that possibility the market is no longer free.