This means that GPIO0, (GPIO1) and GPIO2 must be pulled HIGH (via a resistor) and GPIO15 (via a resistor) is pulled LOW at boot.
In one of my projects I used this as a feature: GPIO0 is connected to a "Function"-button: when it is it pressed at boot, I can upload firmware, at run-time it's just the "Function"-button.
If you don't want end-users to (easily) be able to enter flash-mode, you'll have to carefully think about what GPIO's you want to use and/or in what mode (INPUT or OUTPUT).
The only GPIO's you "Can't" use are GPIO6 ~ GPIO11 since these are connected to the on board FLASH memory.