It's about size of the arbitrary data and its purpose.

Satoshi including a tiny message (a couple of bytes) in the coinbase of the very first mined block in an extremely restricted way (coinbase script size can not exceed 100 bytes) is very different from including any arbitrary data in any transaction in any block at any size without any restrictions.

The fist case doesn't change anything about nature of Bitcoin being a payment system and doesn't hurt anyone. The second case does turn Bitcoin into a cloud storage and is greatly damaging it.