The "lines" button displays a list of lines in the current city. You may check/uncheck the boxes next to each line name to temporarily activate/deactivate a line (when deactivated, the program ignores the line to find a route).
After you exit the program, your selection is lost and the next time you start it, all the lines will be active again.
In large cities, if you press the "lines" button twice, a list of line groups will be displayed (e.g. "subway", "trams", "buses", ...). If you activate/deactivate a group (using the checkboxes), your selection will be saved between uses.
You can use these features to improve the software efficiency. For example, in London, the program may recommend using the Airbus A2 to go from Euston to St.Pancras, whereas the line can be used only to go to or come from the Heathrow airport. The solution: disable the "Airport services" group and reactivate it only when you need to reach an airport.