http://revach.net/article.php?id=4167

Section: Tefila   Category: Bi'urei Tefila
Birchas HaShachar - Why Does The Rooster Come First?
Waking up in the morning is a huge bracha from Hashem.  Our Neshamos are returned to our listless bodies, refreshed and ready to take on a new day.  Yet what is the first bracha that we say to Hashem?  Thanks for giving seichel to the rooster!  Why exactly are we thanking Hashem on behalf of the rooster?

The Talilei Oros brings from the Kehilas Yaakov that really we are supposed to start our day with Krias Shema and Tefila.  These are mitzvos that are dependent on time, specifically they happen at daybreak.  Time is of the essence for if we don't say it on time, the mitzva is lost.

The problem is that it is hard for us to know exactly when the morning is. Depending on where you live time is all relative.   It also depends on weather conditions.  The only absolute proof of time is from the rooster.  He need not see the sky nor read the map.  The rooster can be locked up in a dark room yet he will cock-a-doodle do right on time.  The rooster is our starting gun for the day to begin so that we can perform our most crucial mitzvos.  Before we start we say thank you, Hashem!