Is it permissible to take products from the factory equivalent to the cost of transportation, in the event that the company does not provide transportation for late shifts as it does for the first shift?

The reference for your entitlement to transportation or compensation for it is the contract between you and the factory management. If the contract stipulates this, then you have the right to claim it; otherwise, you do not. This is based on the Prophet's (peace be upon him) saying: "Muslims are bound by their conditions." It is not permissible for you to take anything from the factory's products without the permission of the responsible party. If your right to compensation is established and the management refuses to fulfill it, and you cannot obtain it except through clandestine means (the issue of taking one's right), then you may take your right if you are able to obtain it from the factory's products or other sources, as long as it does not result in harm or scandal. You must not exceed your rightful claim.