One thing that I might think about keeping the money (probably after asking the employer what his stance is about it) would be if I get EU261 compensation due to a delay. Especially if the delay meant I had less free time (ie, I "paid" for the delay by arriving later back home/later on a day to a hotel when I didn't had to work etc. - guess that goes down very much to travel policy of an individual company) that was none of the companies business. I think in that case, the employee should be able to pocket the compensation for himself.