The reasons are two-fold: the city is looking to put more cyclists on Parisian roads in order to reduce both congestion and smog. The city is also planning to build more bike-parking spaces and to develop a better network of bike paths to further the two-wheeled effort. Additionally, many accidents occur from bikes getting caught in drivers' blind spots, so moving those bikes through red lights could prevent such accidents as well.
Similar laws have been considered in the States, first in Illinois and later in Nebraska. The idea is that lighter-weight bikes and motorcycles fail to trigger traffic sensors that are embedded in roads and can speed up a light change when cars run over them. As a result, two-wheelers that have to wait more than a minute or two for a signal to change could be able to legally run the light if the coast is real clear.
Paris is taking a broad approach to reducing emissions from people getting around the city. Besides the bike rule changes, Paris has implemented short-term bans for even-numbered license plates and considered banning old cars from the road.