It was not taken seriously for several reasons. One of them was, of course, that forming such a partisan organisation would indicate that Germany had lost the war.
Thus it ended up being mainly a propaganda stunt - like the myth of the Alpine Redoubt, which was crafted by Goebbels' propagandists in order to give the appearance of a well-fortified redoubt in the Alps, from which German troops could continue the resistance (Kaltenbrunner and Wolff tried to use that myth as leverage during their negotiations with the Americans in Switzerland (Wolff negotiated with Dulles to arrange the capitulation of the German army group in Italy, while Kaltenbrunner tried to arrange for a Nazi government to remain in power in Austria, whilst also hoping to split the alliance)).
Admittedly, the Werwolf was somewhat active. The major of Aachen, Franz Oppenhoff, a German nationalist appointed by the US Army, was reportedly shot by a Werwolf commando and on 28 April 1945 there was the so-called Penzenberger Massacre near Munich, during which the "Werwolf Oberbayern", acting under the authority of Gauleiter Paul Giesler, slaughtered several members of the anti-Nazi Freiheitsaktion Bayern, including a pregnant woman.
There was reportedly also some Werwolf activity in the Sudetengau, but on the whole it was all very uncoordinated and organised very haphazardly - most of the Werwolf activists from the SS, the HJ and the BDM lacked experience and there was a lack of officers to train them (not even SS-Obergruppenführer and General of the Waffen-SS Hans-Adolf Prützmann, former SS and police chief in East Prussia and in the Ukraine, who was their nominal commander, but did not really become active, especially because by the time the Werwolf was formed, the collapse quite swift).
Himmler also did not really concern himself with such a formation, as by that time he was more interested in arranging negotiations with the western allied powers through Count Bernadotte in order to suceeed Hitler as Führer.