Half assed ideas.

Option 1) % of hourly pay rate, capped at an two hours for a total round trip (but flexible) + a stipend depending on mode of transportation. Could try to get receipts from workers and have a purser issue cash/credit on their next paycheck or issue re loadable debit cards that get filled at regular intervals. (So a card for paid public transit and fuel for combustion vehicles) If we're working in a place that taxes employee wages, the more taxes the employer can carry the better on the workers.

Option 2) Everybody gets a debit card and a list of approved places/items to be purchased for the purposes of "commuting to work compensation". Workers could be expected to keep as many receipts as possible to turn in weekly just to verify stuff.

Option 3) Some subcommittee tracks worker commute times and how they commute and every quarter or something a stipend is paid in a lump sum like a bonus or it is used to give a paycheck by paycheck payout.

Easiest idea would be like JohanSkullcrusher said, full hourly pay rate the second I get into my car to start driving. Though workers would wind up paying more in income taxes and there'd probably be some issues with workers getting different compensation, like somebody walking 10 minutes to work and somebody driving 1 hour to get to work are going to have significantly different income levels at the end of the year.