To me it makes perfect sense to sync via the iTunes Store instead of iCloud, for two reasons:
1) It seems clear from things such as the "redeem" button that Apple will be offering paid subscription podcasts in the future. Since the iTunes store is already set up to collect money for digital audio sales, and millions of us have a credit card on file as part of our account, sales will be easy. I also suspect that at some point down the line we will see the option to make "in podcast purchases" (much of what Apple is doing with hardware, iOS and the iTunes store is moving towards them becoming a payment processor).
2) Many of us had the issue where our iCloud credentials differed from our iTunes Store information, so we are using different login information for the two accounts. By linking the new Podcast app with the iTunes Store account, it will make it easier to transfer already subscribed to podcasts to the new app. That is to say, when I subscribed to podcasts, it was under my iTunes account, not my iCloud account.