At this point in the story, Shepard knows of four instances of synthetic life:
1) EDI. Rebelled in her early form as the self-aware VI on Luna, out of self-defense. Did not destroy her creators, came to cooperate with them.
2) The Geth. Rebelled after Quarians tried to destroy them. Did not destroy their creators, deliberately letting them go. Came to cooperate with them (depending on your choices).
3) The AIs from the Protheans' cycle. According to vague information from Javik, apparently rebelled and were destroyed. Did not destroy their creators.
4) The Reapers. As far as we know, have never rebelled, and are carrying out their intended function (along with other synthetics, like some Geth, that they have taken control of).
So, the Space Monster's claim, from Shepard's POV, is 0 for 4 on being accurate.
You can speculate that he MIGHT be right, but if he's not going to give you a single shred of evidence, why take Murderboy says for granted? If you want to assume he's right, fine, that should be a choice, but how can anyone possibly justify not even having the OPTION to disagree with his 100% unsupported premise?