First, you learn what you are talking about.
> Say, I calculated a VaR figure of $100, but the daily loss is often
> larger than the threshold of $100.
No, you calculated VAR of USD 100 with a certain pbability and horizon. If you are often above it then either your parameter are wrong, or you have simple a wrong formula. If you calculate ta 1 hour VAR horizon, then naturally the daily loss will often be higher. If you calculate a 80% horizon, then one of 5 days will be outside, even without black swan type event.
Second, it is useful as a generic measurement of how much risk you ahve, not as the all end of risk management (as the outlier will come nad kill you - have a 95% var, that is 5% outside, and out of that some small 0.5% will be NASTY).
But a VAR has alyways 2 parameters - percentage and time horizon.
http://en.wikipedia.org/wiki/Value_at_risk has some explanations.