The brain drain effect is pretty serious here. Why wouldn't I want to go somewhere where the other smart people are, and where I can pretty much wear shorts 10 months out of the year? Culture/politics aside, the US is still one of the best places to live if you have money.
There is little venture capital available to computer/software startups. The few incubators in Canada have ridiculously terrible terms -- eg. 20% equity for a seed investment. Most Canadian startups look to the US for investment, or move to SV if possible.
The TSX and TSX Venture stock markets are entirely geared toward energy & alternative energy companies. If you intend to go public you'd probably have to move and re-incorporate in the US.
The Canadian government is generally not very supportive of (non-energy) technology companies. Most small business incentives are only for large-ish companies that want tax breaks for investing in solar & wind energy.
If you look at many SF and NYC startups, as well as Facebook, Yahoo, and Google's rosters, you will find many Canadian tech entrepreneurs - maybe even moreso than within Canada itself :)
There was also historically issues with Canadian startups getting foreign investment / selling to a foreign company, although that situation is now changing.
For general info about the Canadian startup scene check out http://www.startupnorth.ca/
Salaries aren't as high as NYC or SV, although the cost of living is also much lower.