Okay, let’s just have a look at this from your original premiss “Ok so ... this seems plausible to me that ... there is an agenda to make people feel insignificant and to carry on about their about their busy lives not questioning anything and being good wage slaves.”
Before, back in the day when the Earth was flat for everybody, did they feel different, more special? And if they did, (due to presumably, a deity) How did this make them more open to questioning their surroundings?
With religious teaching there is the attendant concepts of Apostasy and heresy, whereby if you reject your teaching or interpret them differently from the norm you are subject to “interrogation”. Often in the past (and in some religions now), one or both would lead to excommunication for the questioner or death.
Now scientists can get pretty pissy if their pet project is superseded, but the only time I can remember that they died for their investigations per-se was at the hands of religion, so where does your impression that science is anti-questioning come from, as the converse is true.
The Royal Society's (one of the earliest dedicated science institution) motto 'Nullius in verba' is taken to mean 'take nobody's word for it'. The very essence of enquiry.
As for feeling insignificant, well I can’t help you much there, if you need a tyrannical father figure making constant demands to have any sense of self-worth then you are made in a different way to me, the universe is vast and to all intents and purpose, timeless, but without me it would seem empty.