Julie had a good point in one of the comments below. The basic point was that there are times when the money saved is not worth the time spent. I definitely agree. But, as Julie implied, the equation changes when there is more value gained than just saving money.
When I make something from scratch, I'm often saving myself a trip to the grocery store. I hate to shop. So if we don't have it, I figure out how to make it. It almost always takes less time and money to do it myself than to go to the store.
Now, you could argue that if you were very organized that you could just go to the store once a week and always have what you needed on hand and not have to cook from scratch. This is a fair argument, but I'd love to hear from someone who actually can do this. Is there anyone who doesn't ever run out of or forget something? I'd love to know your secret if you don't.
I also place a high value on being home. This isn't something a lot of people value, I know. But I like it. I'd much prefer to keep track of my boys at home than at the store. I feel much more independent at home. It's where I belong.
As a result of combination of these little quirks of mine (liking to be home, hating to shop, a flair for cooking creativity), we've been able to go without a second car since we've been married. That has been our real savings- easily $10,000 or more over the last 7 years. Even though it doesn't really save a lot to make tortillas, or applesauce, or refried beans, it's the way it all comes together that saves us the money.
There are some things I don't do. Making my own bulgur was way too labor-intensive. I didn't do cloth diapers. I don't have a cow. There are a lot of things that really aren't worth it to me.
But in the end, beyond saving money, I just like homemade food. I like homemade tortillas and the 20 minutes that I spend rolling them out while chatting with my sister on the phone is worth it. I like that I can make healthier bread. I like fresh yogurt. I guess it all comes down to flavor.