Why Nios II don't execute my ISR?

Also take a look at the "Hello Freestanding" software example in the IDE. Basically this is the same as what monkeyboy is suggesting (that is, the example source code performs the same functions that our alt_main.c does), but is provided as a ready-to-modify documented software example. The code in Hello Freestanding performs all the normal stuff you get with starting in main() -- you can then modify it as you see fit to reduce code size. One of the things in the freestanding example is calling alt_irq_init() as monkeyboy mentioned.