Why??

I can't presume to know exactly why these beings would want to keep their presence hidden or why TPTB would go along with their agenda, not for sure anyway.

I do have some theories, though.

I believe that we (human beings) are really nothing more than their lab rats, their guinea pigs, their genetic experiments, their chattel.

I believe that our leaders go along with what is happening because they have little choice.

I believe perhaps they have negotiated with these beings some kind of treaties that allow human beings to go along largely unmolested and harassed in exchange for government secrecy and cooperation with their agenda.

I believe that our government is getting access to technology far above and beyond what they release to the public.

I believe that our government is genetically experimenting on humans and allowing other beings to do the same. 

I believe these beings have infiltrated the highest level of human government agencies.

I believe that the true knowledge of these beings and their association with out government is kept closely guarded.  I believe that only a few high level government officials have access to the truth, and I believe that these people are closely guarded.

I believe that many of the widely believed and circulated so-called 'conspiracy theories' are disinformation campaigns created, manipulated and monitored by government agencies and other beings to ensure that humanity never gets too close to discovering the truth.

I believe that religious belief is encouraged because it further keeps people from understanding their true origins and investigating their actual place in the hierarchy of lifeforms on this planet.

I would not be surprised if modern man is a genetic hybrid or creation engineered by these beings for scientific research and perhaps breeding purposes.

I think that there are likely several breeds or factions of these beings living on this planet, some more benevolent than others.  I believe that, perhaps, some of these beings offer protection to humanity from some of the more malevolent beings in exchange for the cooperation of TPTB.

I would not be surprised if these beings orchestrated mass cullings of humanity as suits their needs, and perhaps TPTB are guaranteed immunity from these cullings for themselves and/or their families in exchange for cooperation.