Couple of reasons for media hate:
1. Niners dominated for so many years. Media members get jealous.
2. Harbaugh is universally dispised (well outside of SF atleast). When I mean dispised I mean DISPISED. People don't want to give him any credit and frankly hope he burns in hell.
3. East coast bias. This will never go away.
4. Teams with a defensive strength are deemed boring.
5. Alex Smith is a popular fall guy.