The vote wasn't actually determined by pro-gay marriage or anti-gay marriage activists, it was determined by the people who were ambivalent and didn't vote on the issue at all.
The pro-marriage side had more funding than any other social cause in history, but they couldn't get the people who didn't care to get off their behinds and actually vote. More people didn't care either way, and not caring is the same as abstaining. So what do you get?
The people who are truly dedicated to making sure the measure goes through will go to the polls because, well, they are hardcore about it. The people that want to stop it, mainly gays and special interest groups, also show up, but they are a minority.
Voter apathy does the most damage. Additionally, in California, no one anticipated Obama's black heritage to swing the vote to the right. Blacks and hispanics, statistically speaking, tend to be of a lower economic class, and so don't come from the educated elites that would vote against the bill. In other words, more people who voted based on their irrational biases showed up to vote in favor of the bill.
I'm of the opinion that the State legislature should override this, as it's a minority issue. Segregation ended, not because of voters, but because of law makers. Minorities don't have the power of numbers to win over rights, they need law makers to help them. Gay marriage does not intrinsically infringe upon the right of heterosexuals to marry, so there is no logical course of action but to create a pro-choice environment where you can marry whichever gender you want.
I do also agree that this bill is a violation of the 14th Amendment's Equal Protection Clause. If gender of attraction/romantic interest is inherently not a choice - and science has already established it isn't - then the amendment is a violation of civil rights as it prevents couples from marrying according to their natural behaviour. Additionally, this amendment violates freedom of religion, since there are many churches in California that have willingly married gay couples up to the present according to their beliefs. Now those churches cannot issue licenses according to their faith.
Finally, the veil of the law does not prevent people from getting married. They can and still will, so the "institution of marriage" is already being "violated" anyway. The amendment simply removes the legal benefits, which is really the only benefit of recognition of the law anyway. Now gay couples with children will not be able to raise their children as effectively as heterosexual people (i.e. lack of health benefits, guardianship if one of the parents dies etc.), which in turn damages family values; couples will not be able to share insurance responsibilities, mortgages, and licensing procedures, because the state does not recognize their marriage.
This amendment is more damaging to society than it is productive, all because of a section of society that believes it contradicts their religious and/or moral values. It will be interesting to see how this situation develops.