That's one of the biggest reasons that laws have publicly disclosed punishments associated with breaking them: they dissuade other people from breaking the law. If the penalty is low, and not because the people of California said that Uber should not be penalized (which presumably they can easily do), that communicates to everyone else who might want to break similar laws that the penalty will be equally low for them.
That, and also laws protecting ethical business practices of the taxi cab companies, which are often unprofitable but desirable for the city population. And also laws protecting employees. And tax codes.
It's true that Uber managed to stir the pot, and definitely helped in fixing the stagnation of taxi services sooner. But that doesn't excuse their flippant attitude towards law and society, or corrupt example they give to the future startup founders.
If you want to change an entire industry, then yes. Sometimes it's better to ask for forgiveness than permission.
Uber has opened up the ride-sharing market to many more people. You don't need a $1,000,000 medallion to make money as a driver any longer.
Since the monopoly has been forcibly broken, it also created competition, which in turn lowers the price for the consumer.
It's a win-win. They are only breaking laws protecting unethical business practices of the taxi cab companies.