ANSWER: There are a few different ways of looking at this. First, let's take the purely doctrinal. From that perspective, there is a critical difference between the Civil Rights Act of 1964 (which regulates commercial activity directly--the operation of a hotel or restaurant) and sec. 13981 of VAWA (which regulates a form of assault). The former is a commercial activity, the latter is not. The majority sees this distinction as dispositive. You could also package this as "attenuation," as the connection of the regulated activity in Morrison to an effect on interstate commerce is at least once removed when compared to that in Heart of Atlanta or McClung. The Civil Rights Act directly and immediately shapes commercial behavior (who businesses must serve). The effect on commerce in Morrison is more attenuated. But, as I indicated last night, this seems like simply a different way of expressing the idea that the activity actually regulated by 13981 was not itself economic or commercial.
Second, as to timing: Yes, political time clearly is also an explanation. In 2000, there were 5 justices on the Court willing to curtail Congress's commerce power. In 1965, had 13981 come to the Court, I feel confident that the Court would have upheld the Act. As lawyers, we can distinguish the two cases (as I have tried to do above), but as Court observers we have to admit that the personnel on the Court at any given moment does a lot to explain how that doctrine is understood or construed -- at least at the margin.