How can the sin of evading public transportation fares be compensated for? And is it permissible to give charity instead of money taken unjustly?

If you are able to reach the driver or his heirs, you must pay them the fare or seek their absolution, and your responsibility is not discharged by giving charity on their behalf. However, if it is impossible to reach them, then you should give the amount in charity on their behalf. If you do not know the exact amount of the fare, then exert your best effort to estimate an amount that you predominantly believe will cover the right or exceed it.