I know I'm a bit late to the party but I'd like to give my take on this considering my understanding of the show is a bit less literal than the rest.
So throughout the two seasons we get to see the life story of Tomoya as well as other characters. The story is composed of many fun and happy moments but also some very sad and painful ones.
At the end of the show Tomoya goes through very rough times and just when he's about to break he is given a choice:
"Would you like to go back and redo everything from the moment you met Nagisa and not go through all that tough things as well as all of the happy moments or are you glad you got to live the life you were given despite everything?"
After that we get to see a much happier version of the world were everything went well and none of the bad things happened.
So basically to me Clannad can be summed up like this: Life can be very beautiful or very sad either way don't ever let those terrible things stop you from living life at its fullest.
Clannad teaches you how to live life and that's why it's is the best anime to have ever been created.