Is it bad if the CO2 bubbles from the diffuser are reaching the water surface?
No, this is normal. The key is to place your CO2 diffuser as low as possible in the aquarium. When the bubbles are released from the diffuser, they imperceptibly get smaller and smaller as they rise and the CO2 gas is being absorbed into the water.
For more information on CO2 systems in high tech planted tanks, read the full article.