can they raise the terror threat level just for mass transit?

You may have asked this question, as I did, after hearing that the Department of Homeland Security raised the threat level to orange for mass transit following the London bombings. I don't think the color-coded system means a lot in the first place, but I did wonder if they were even following their own internal logic (a single threat level for the entire country, or at least a region).

They are -- the rules of the system say that the threat level can be raised for specific industries, and that would seem to include mass transit. However, it should be noted that the entire country, rails and all, stayed on yellow after the Madrid bombings, which (at present count) killed about five times as many people. You could argue that they know something we don't, but the DHS site says there is no specific threat at this time.