Is the beneficiary of company transportation considered sinful if she does not submit a request and pay the symbolic fee?

Using company transportation without paying its prescribed fees is impermissible. It falls under the category of consuming people's wealth unjustly and through deception. It has been reported, "Do not commit what the Jews committed, lest you make lawful Allah's prohibitions through the slightest of deceptions." Therefore, one must repent to Allah and pay those fees to the company, unless the officials or owners pardon you.