The second issue I ran in to was that I found myself huffing and puffing along as I worked on the longer runs. Sure, running 60 seconds at a 10 minute/mile pace and then walking for 90 seconds allowed me to catch my breath in between each set, but in the end that isn't sustainable.
There are a few things to keep in mind on this, and the first is that during the C25K program your muscles will change and grow to allow you to run longer, but your lungs won't change much, and they are what you need to run faster. The rule of thumb for runners of any distance is that if you want to be able to keep it up, you should be able to carry on a conversation as you run. Not necessarily as easily as you would if you were sitting at the dinner table, but you should be able to talk. If you're running alone, try talking to yourself.
Once you find a pace that you can sustain, you will want to keep working at that pace. That may not seem necessary for the 90 second or 3 minute runs, but you will thank yourself (and me) for it later on when you are running 20 minutes at a time.
There is absolutely no shame in going slow. You're just starting out and nobody expects you to be fast. The phrase I've come to adore when I feel slow is this: "No matter how slow you go, you're still lapping everyone on the couch."
My own lack of speed can be epitomized by the fact that in both 5K races I have completed so far, I have been passed by visibly pregnant women. Realistically, though, I am carrying much more than they are in terms of weigh, so it's reasonable from that perspective.