This question, along with a number of articles on the Internet, misconstrues what the rule change is about.

The rule change does not say that you can get a search warrant, that is to enter premises with/without machineguns etc, solely on the basis that someone is running Tor on that premises. The rule changes actually has nothing to do with search warrants.

The rule change is about "remote access" warrants and, specifically, the question of which magistrate you need to get the warrant from.

The background is that statute grants the FBI the power to hack into a computer (that is, obtain "remote access") to search for and retrieve evidence in a criminal investigation. One of the preconditions for doing so is that they identify which district the computer is in, and apply to a magistrate in that district. (By way of further background, under the American way of distributing power, it is seen as a bad thing for (for example) a magistrate in California to be able to issue a warrant to an FBI agent to conduct a search in North Carolina.)

When the target computer is desired to be hacked because it is running a hidden Tor service, then how does anyone know what district it is in? Where does the poor FBI agent apply for his or her warrant?

This rule change resolves this practical problem by saying that, where the use of Tor or a similar system precludes any knowledge of the physical location of the target computer, then the FBI can apply for a warrant with any magistrate.

See further http://www.fed-soc.org/blog/detail/amendments-to-federal-criminal-rule-41-address-venue-not-hacking-powers