All perfect praise be to Allaah, The Lord of the worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad, sallallaahu ‘alayhi wa sallam, is His slave and Messenger.
It is permissible for a Muslim to perform Hajj at the expense of relatives, co-workers, friends and others. So, if the company in which you work bears the expenses of Hajj for its employees from a fund that is based on deducting shares from their salaries with their permission, then it is permissible to accept this even if there are non-Muslim employees among them. In this situation, the end result will be that a non-Muslim granted money to a Muslim who may accept it and use it in Hajj or anything else.
What really counts in such a matter is that the money is paid with the permission of its owner, regardless of him being a Muslim or not. Furthermore, the money itself must be lawful so the fund should be clear of any usury-based investments or prohibited contracts because Hajj expenses should be covered with lawful money.
Allaah Knows best.