Why is it frisst and not isst?
You use fressen for animals and essen for humans.
I thought it was der Vogel. Whats the difference with den Vogel?
Den is the accusative (akkusativ) case of der. Der, Die, Das get changed depending on the word order to it's respective case. http://german.about.com/library/blcase_sum.htm
When does frisst mean 'eats' and when does it mean 'is eating'? Do we have a rule here that I might have missed?
In German, they dont use the present continuous tense oft. So, whether to translate as "eats" or "is eating" depends on the context.