Karune has finally officially addressed this issue which has concerned many fans since rumours and hints of the monetization of battle.net 2.0 began to surface. While some aspects of the new system may be require a fee, simply playing the game online will be free. Karune had this to say:
Blizzard Quote: (Source)
When a player buys the StarCraft II box at retail, they will have the ability to play on the new Battle.net for free.
For those listening to the latest Activision Blizzard conference call, Mike Morhaime also mentions it there as well.
If you buy the game, you can play online for free; the way things should be.
Karune also addressed concerns regarding the matchmaking process. He ensures fans that high skilled players will be matched against challenging competitors while lower level players will be matched against opponents of similar skill.
Blizzard Quote: (Source)
Making sure players of all levels are able to have a fun multiplayer experience is a top priority for us. More info regarding this effort will be revealed in conjunction with info on Battle.net. For now, know that if you don't have 300 APM...it’s quite OK. We've got plans to keep online play fun and challenging at the same time, while also making the atmosphere feel less intimidating for the vast majority of us who aren’t pro-level players.