It is just a quirk of the app that a straight line (one with only two end nodes) can't be added to another shape -- regardless of its stroke width, it is considered to enclose no area, so it doesn't add to (or subtract from) any other shape it is combined with.
There are several ways around this, the simplest one being to use the Expand stroke option on the Layers menu, but since the Expand stroke command usually adds extra nodes, it may not be the best one. Another alternative is to substitute a thin rectangle or rounded rectangle for the line, positioned & rotated as needed. This will create a new shape with the minimum number of nodes needed.
geometric Boolean operations can be applied only to paths that enclose an area, which means you cannot add (intersect, subtract, etc.) a straight line and a rectangle, for instance. But you can always use Layer > Expand Stroke to create a closed path from your straight line and apply a Boolean operation to the result afterwards.
