Many analysts, across the spectrum of political belief, claim that Mr Trump engages here in what is termed dog whistle political speech. In the same way that a dog whistle produces a tone which is audible to a dog but not to a human, dog whistle rhetoric carries a specific meaning which is clearly understood by the targeted audience, but which is sufficiently ambiguous that listeners outside of that targeted audience will not perceive it as they do.
In this case, the targeted audience is assumed by these analysts to comprise those Americans who believe that the Presidential candidate Hillary Clinton is planning secretly to deprive them of their rights under the second amendment to the United States Constitution, which prevents the government from infringing upon their right "to keep and bear arms."
The aforementioned analysts deduce that the candidate here infers that the Second Amendment people (Americans who zealously defend that right and who own firearms) may be able to punish Ms Clinton should she be elected to the Presidency and succeed in her alleged plot to appoint Supreme Court justices who would somehow revoke the Second Amendment. Implicit in their deduction is the unsupported belief that the Second Amendment people are willing to employ violence in defense of their rights under that amendment. The dog whistle in their analysis is the unspoken threat that this punishment will be effected with firearms: that she (or the Supreme Court justices whom she might appoint) will be shot.
Mr Trump and his supporters rejoin that he intended to imply nothing of the sort, and that his statement was merely an admonition to vote against Ms Clinton.
I couldn't do it without X is a common way to acknowledge X for its contribution to the success of the speaker's projects, endeavors, career, etc.
This is often heard during acceptance speeches given at awards ceremonies.
Example.
I'd like to thank my mom and dad. I couldn't have done it without them!
Neil Patrick Harris (NPH) is a famous actor. Here, it sounds like he is acknowledging the "little people" for their support. Here are two definitions of little people from M-W:
little people
: ordinary people who are not wealthy, famous, or powerful
: people of unusually small size
In this context, I take "little people" to mean people that don't usually get credit for their work, people who work behind the scenes, like writers, costume designers, camera operators, etc. and the many fans.
Further, it might be a play on words. I believe little people is currently a politically correct term for people with dwarfism. Little people are often cast to play elves in Christmas movies. So if there were elves helping NPH in the movie, then he's specifically acknowledging them for their help.
By the way, I couldn't find part of the conversation in this copy of the script. I assume that OP heard correctly though. Throughout their interaction, it seems like NPH is dismissive of Jesus Christ. So "Thanks. Couldn't do it without the little people." does not seem to be directly related to Jesus's statement. He seems to be ignoring Jesus, unwilling to believe that it's him.
Best Answer
The argument in that paragraph is that "WE" make the mistake of thinking such people (e.g. professors and elders) are 'without substance', which means they are without enough intellectual capacity to present the idea directly.