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the security and the sense of IPN system

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the security and the sense of IPN system

Hey guys.
I've been trying to implement your Paypal's IPN system and I have a few questions. Note, I'm not a backend developer and so my knowledge is limited.

So the question one is: why do we use IPNHandler.php (as noted in your docs and github account) ? What is the purpose of that script, since I've used IPN simulator and well it always returns that handshake was made (so it's sole purpose is to check whether the domain is valid). How does this authenticate anything from letting a random person use our 

http://mydomain.com/paypal/ipnHandler.php

?

 I just can't seem to figure out why does this authentication takes place and how does this secure any connection made.