Is it permitted to have not-religious guests who come before Shabbos knowing that they will leave on Shabbos via public transportation (despite being offered a place to stay)?
If it is certain that the guests will be leaving by public transportation, it would not be permitted to invite them to the Shabbos meal, because this would involve the prohibition of lifnei iver lo titen michshol (carrying the money for public transportation could be a full Torah prohibition). However, when inviting the guests, they can be politely asked to walk home after the meal (if this is possible, or to stay for the entire Shabbos if this is not possible), in order to avoid a desecration of the Shabbos. If their method of going home is unclear, it would be permitted to invite them for Shabbos, and, indeed, a mitzvah to do so, seeking to draw them closer to their roots.
Sources: See Iggros Moshe, Orach Chaim, vol. 1, no. 99; Chashukei Chemed, Pesachim, p. 189, in the name of Rav Elyashiv shlita.