In chief Rabbi Rav Yitzchak Yosef's weekly shiur last night he related to the issue of the rail authority doing a lot of its work upgrading and repairing rail lines on Shabbos.

Obviously that is not allowed according to halacha, but the question is how it effects whether we, the passengers, are allowed to benefit from that chilul shabbos - can we ride train lines on which we know work was done on Shabbos?

Rav Yosef concluded his shiur by sayng that it is clear from Shulchan Aruch that we are allowed to ride the train during the week despite knowing that work was done on the lines on Shabbos - even on that same specific line. For example, despite my knowing that work was done on Shabbos on the Kiryat Gat line, I can still take the train to Kiryat Gat on Tuesday (for example). That is clear halacha in Shulchan Aruch Orach Chayim.

The Chief Rabbi added that while this is basic Shulchan Aruch, there is room for the 5th volume of Shulchan Aruch in which the gedolim might possibly decide on imposing a fine on one who desecrates Shabbos, in order to discourage them, or even force them, to stop the Shabbos desecration. That is a different issue, but until they do so, the SHulchan Aruch allows us to ride these trains during the week.
source: Kikar