Yes and no. It takes a little explanation of muscle physiology to clear this up.
We all know that muscle adapts to heavy weight by growing bigger and stronger, but it also adapts to aerobic training. To make the muscle more efficient at receiving vital components to its energy production, it actually shrinks in size. This is not a bad thing, if you are training for a marathon. It makes the muscle work much better, but obviously if your goal is to put on muscle size this is a bad thing. Thankfully, your muscles won't shrink due to a 30 minute cardio session. Cardio for health or fat loss will not hurt your muscles.
Performing multiple 10-k's a week will. Take a look at sprinters vs. Ironman triathletes. Sprinters are always muscular and lean, while Ironman triathletes are lean but often small and stringy.
Remember, cardio is just as healthy as weight training, and when used in moderation will not hamper muscular gains.
You say you have a 30 - 45min window of opportunity to take protein, etc. after working out. Does this mean 30 - 45mins after a complete workout, or does this mean 30 - 45min after working out a single muscle group?