Rabbi Frand quotes The Sanzer Rebbe, zt”l, so once said that this is
the meaning of a universally practiced custom.  

 The Gemara in Brochos says that Rabbi Yehudah HaNasi put his hands over his eyes when he read Krias Shema. That is the way everyone reads Shema Yisrael. Why do we do it that way? The Sanzer Rebbe explains it is for this very reason. It symbolizes our inability to perceive the fact that the Midas HaDin and the Midas HaRachamim all come from the same source.  

We can’t see the Attribute of Mercy being the ultimate source of bad things that happen to us. Therefore, we cover our eyes: I can’t see how this could possibly be good. I can’t see it – but I believe it! 

 If we look back at Jewish history, this is even harder to believe than personal life experiences which may trouble us.    

On the national scale, the things thatKlal Yisraelhave endured are
mind-boggling. They are hard for the human mind to understand.  

Therefore, when we recite Krias Shema, we need to cover our eyes, because many times in this world, we simply cannot see the unification to which we are testifying – thatHashem Elokeinu Hashem Echad, that it all stems from the same Midas HaRachamim.