Why are Arduino timer registers not 0?
The Arduino core does things at startup. One of those things is to configure the timers ready for PWM operation.

Here's the relevant bits from init() in wiring.c:

    // set timer 1 prescale factor to 64
    sbi(TCCR1B, CS11);
#if F_CPU &gt;= 8000000L
    sbi(TCCR1B, CS10);
#endif

#if defined(TCCR1A) &amp;&amp; defined(WGM10)
    sbi(TCCR1A, WGM10);
#endif