Imagine a guy is mining a second blockchain since block 2
Now imagine he manages to make it longer (by mining or by finding a flaw in the mining process) that the one we currently see and he releases it
Result: all transactions are reverted and the only one to have any bitcoins since block 2 is him

By adding a checkpoint at block n, you force your client to refuse chains if the hash for their block n is not the one of the checkpoint, so the guy can't revert the blocks older than n