Budget, are you thinking a 'big' present or more stocking fillers.
For big present, I'd go really good bluetooth noise cancelling headphones, I have Bose QuietComfort and they are brilliant, used every day on the tube/train (only issue is they're so good I've more than once missed my stop on the tube). Or alternatively, a really nice stylish but comfortable and roomy bag particularly if s/he has to carry a laptop around with them. Or perhaps a Kindle or tablet for reading or watching TV on the train, if they don't already have?
Smaller things I use every day, my 'keepcup' reusable coffee mug, mine is insulated so I fill it in the morning before getting on the train and the coffee stays warm all journey, I often use it to grab a coffee in the office and/or on the way home too without having to use a takeaway cup. Or on a similar theme, how about a gift voucher to their favorite coffee shop (can you sense a theme, coffee is absolutely essential to my commuting sanity lol!)
I also have a nice matching insulated waterproof lunch bag that is nice to bring lunch in from home and keep cool all day - or you can get lovely bento style ones with compartments for different foods?
I also always carry my little slimline battery pack so I never run out of phone juice on my journey (my worst nightmare, that and having no coffee😱)
Other ideas, I spend a lot of time on my commute on apps of various kinds, list ones for chores and life admin, food ones for diet purposes, health ones to track exercise and step count, game, puzzle and podcast ones to pass the time, you could find out which ones your commuter likes and pay for upgrades if available? Or how about an audiobook subscription for them to listen to on the commute, or a digital newspaper/magazine subscription?