Most companies are afraid of open source software, as anyone could write in or find (by reading the source) a back door or security exploit.
Also open source hardaware/software often doesn't have the same level of support as hardware/software you buy.
Arduino can be used for commerical use, but it won't be arudino's fault if your project breaks something or hurt someone.
(Some linux distributions and things like apache are major exceptions to the above)