Exactly. Reputation is supposed to illustrate your expertise. If you gain 1000 rep points in the cooking SE, does that mean that you should have 1000 rep points

Exactly. Reputation is supposed to illustrate your expertise. If you gain 1000 rep points in the cooking SE, does that mean that you should have 1000 rep points in the programming SE? Of course not, since your expertise is with cooking and not programming. If you were to carry across reputation from one SE to another then it would make the reputation meaningless. Instead of being an expert cook with 1000 rep points you would be an expert SE user with 1000 points that might have come from answering questions about cooking, programming Ubuntu, startsup, etc. Now THAT would break the system.