The nebulous Nazi connection lives on or so it would seem. Even this Guardian article openly admits the connections between the American formed post-war German intelligence services and ex-Nazis. The question is, as Neo-Nazi groups have acted and continue to act (often with impunity) are they being facilitated by the state intelligence apparatus? It would seem so.
But why? Is this explained by crypto-Nazi sympathies within the German Establishment? Clearly then and now the US intelligence services all but dominate their German allies and with modern surveillance dragnets it is almost inconceivable that US signals intelligence is not able to aid German agencies in apprehending these figures. If it's a rogue element within the German services, the tools are there to stop them and yet it's not happening. In fact it would seem they're being protected.
During the Cold War the United States eagerly employed these elements, often actual Nazis (as opposed to Neo-Nazis) to serve its purposes in the struggle against the Eastern Bloc. The various Neo-Nazi movements have had an ambivalent and often bitter relationship with the West and yet clearly the West German (and now German) intelligence services were and perhaps are helping them. Was this under the nose of the Americans or (in some cases) at their behest?
Why would the United States facilitate the Far Right in Germany? For the same reasons they have done so elsewhere in Europe. It's the strategy of tension, the fueling of social and political strife to drive the politics and manipulate both the democratic impulse and the process.
Despite the rather suggestive evidence it could still be maintained that it's simply Nazi sympathisers within the German apparatus that are allowing this xenophobic violence to continue and this is being done outside the purview of the United States. But it doesn't seem likely to me. Precedent I think should be our guide or at least the default presumption.