During the opening cinematic, you see the boy outside, playing with a Normandy toy. If he has a Normandy toy, he knows who Commander Shepard (your character) is. If he knows who Shepard is, then he knows what he/she looks like. If Shepard tries to save him, he'll let Shepard save him.
If the boy had allowed the player to help him out, then gamers would not have had to witness the shuttle he boarded get incinerated by a Reaper. That death haunts Shepard's dreams throughout the rest of the game and is the reason why the Catalyst (a sentient being that controls the Reapers) decides to take the form of that young boy.
Had this one thing happened (the kid accepting your help), players would not have had to sit through multiple, repetitive dream sequences (that were a missed opportunity) where you are forced to "run" incredibly slowly, chasing the boy around a forest until he disappears in flames. Shepard would have been in a better state of mind throughout the rest of the game as well.
Many Mass Effect fans also hated the ending (I held out as long as I could, but eventually joined them in their rage.) If the Catalyst chose a different form, then at least one part of the much-hated ending would have been different.
Lesson: If you are hiding in an air vent and the hero of humanity and all of the galaxy offers to help you, say,"YES!"