Maybe you've set your maximum population capacity to 100, if you increase it, it might work then.

I play a lot of AOE3 at lunch at work and can confirm that you don't get a higher population limit for extra town centers.
However they do mean you can produce village more quickly by making some at each town center. For booming (economy) You want lots of villagers. Also, as YA said, it makes it harder to destroy you if you have more than one means of production. I tend to boom and then towards the end I can field large armies very quickly and re-create them as often as needed. But early on you are very vulnerable, spreading out can help a lot.

Well, I have my own litttle stratedgies, but mostly the game's on easy ^^;;;
Better than sandbox...
But I always survive. I usually have at least... 41 villagers (another 10 our boats) and they are able to take out a few hussars and also a musketeer or two (even though most of my opponets only send out meleee units). Besides, once I reach the colonial age I bring in the military. If I'm at sea I always bring in three galleons to make sure the enemy cannot steal me fish and whales.
I almost did beat a game on moderate, but then my monitor died and their was a lot of cussin' that night... It was a good match too... Russians vs. Spanish... they were so pathetic... my cannons blew 'em away when they got to close over the river... pathetic fools....

hehe I play against the rest of my office so it little more interesting with real people ^^