In Aldous Huxley's Brave New World, Bernard Marx is a self-serving person who brings John the Savage back to the New World in order to advance himself and put the Director, who is John's real father, into a compromising position because he has threatened to have Bernard exiled.

However, things do not go as Bernard has planned.  So, in Chapter 16 when Mustapha Mond calls Bernard and the Savage in after the incident at the hospital, he asks John if he does not "like civilization," and John frankly answers no:

Bernard started and looked horrified.  What would the Controller think?  To be labelled as the friend of a man who said that he didn't like civilization--said it openly and, of all people, to the Controller--it was terrible.  'But, John,' he began.  A look from Mustapha Mond reduced him to an abject silence.

As Mond continues to interrogate John, Bernard sinks into "a yet more hopeless misery."  Clearly, then, Bernard is pusillanimous and only interested in saving himself from any situation.  So, in Chapter 15 when John attempts to bring freedom to the "khaki mob" by throwing out their soma and urging them to think for themselves, Bernard whispers, "He's mad....They'll kill him.  They'll...." and he worries for himself.  But, suddenly, Helmholtz is at the side of John, demonstrating the sharp contrast between him and Bernard.

"They're done for," Bernard thinks, but he does run forward, "urged by a sudden impulse."  However, he

thought better of it and halted; then ashamed, stepped forward again; then again thought better of it , and was standing in an agony of humiliated indecision--thinking that they might be killed if he didn't help them, and he might be killed if he did--when (Ford be praised!), goggle-eyed and swine-snouted in their gas-masks, in ran the police.

Indecisive and weak, Bernard fears for himself.  And, in truth, he does not really wish to rebel completely as his exclamation--Ford be praised!--indicates.

There is not a clearly stated reason -- it does not say "Bernard hesitated because..."  However, I think it is safe to say that he hesitates because he is not eager to fight against the rules that the government has set up.

I think he is physically afraid to some extent.  He does worry that he might be killed if he does not jump in.  However, I think that he is also not that much of a rebel.  That is one reason why Helmholtz jumps in and starts fighting -- he is more of a rebel.

We will also see this when the two of them are told they will be exiled.  Watson is fine with it, Bernard becomes emotionally distraught.