Anaphora is the repetition of words, phrases, or lines in a written work, and even a cursory reading of Allen Ginsberg's iconic poem "Howl" reveals his consistent use of this technique to emphasize his themes. Your question specifically asks about madness and the resistance to government, and those are not difficult to recognize in this poem.
The first part of the poem is primarily concerned with the madness portion of your question, though of course each person listed as mad here is also doing something to resist, if not government, then at least the perceived rigid structures and institutions of society. The anaphora in this section is the phrases beginning with "who," all of which refer back to the opening line of the poem:
the best minds of my generation destroyed by madness, starving hysterical naked....
Each of the people listed in part I are types, amalgamations of the people Ginsberg has seen turn mad because they had to find a way to escape the restrictions of society; and he portrays them all as innocents who have been victimized by the world in which they lived. Notice that they almost all turn to drugs as an escape from what they perceive to be the things which confine them: universities, business, metropolises, "hospitals and jails and wars," religious institutions, city hall [government], commerce, transportation, Capitalism, the FBI [government], entertainment, infrastructure, and money.
While this list does not only include government as the things which these so-called brilliant madmen were rebelling against, everything on the list is connected to the government in some way. Clearly Ginsberg has a point of view which says that all of these things are detrimental to the free-thinking genius types about whom he writes, and their only escape was through drugs (though he does not seem to fully condone their excessive drug use, either). The anaphora serves as a kind of piling on for effect--not just one "best mind" was destroyed but a long and varied list of them. His assertion is that it was government-run society which caused every one of these tragic losses--every "who" in this list.
In part II, the anaphora is "Moloch," something Ginsberg called “the monster of mental consciousness.” The word works as a kind of a chant and a curse, and the chant is raised once again against such societal structures as banks, factories, war, and industries, Again, these are all things connected to government, not madness, and to those who choose to see a capitalistic society as the enemy. We do get one specific reference to government, and it comes in the form of a curse:
Moloch the stunned governments!
Finally, part III of the poem is concerned about Ginsberg's friend, someone he considers to be a victim/hero who is also a psychiatric patient. The anaphora is the line "I'm with you in Rockland" and refers to Rockland Mental Hospital and this madness. While this stanza does make references to war, religion, and even revolution, the connection to government is most tenuous in this part. The implication is clear that Carl Solomon is still battling against the world, but the anaphora focuses more on Ginsberg's commitment to his insane friend and even his cause than to any kind of statement about resisting government.
It is evident that Ginsberg's motivation in writing this poem is his disdain for the society he is living in, something he considers to be restrictive, confining, and antithetical in every way to creativity and individuality.