You can get free banking if you maintain 3000 euro in your account at all times.
If you don't qualify for free banking, you'll be charged at least 11.90 per quarter - for the first 90 transactions, even if the actual number of your transactions is going to be much smaller. At least that's how I understand it. And yes, I agree, it's a rip off in cases when only a few transactions are made (or none).
There is still an option for Pay as you go which is 28c per tx (and has been 28c per tx for a long time contrary to popular misconception). If you have only a few transactions then this is the cheaper option. You just need to tell your bank that you are taking this option. If you are alrady on it no need to change anything.
To answer another question ...yes Phone top ups do count as online transactions.
There is so much media frenzy about this and so much false information. Yes I am a staff member of BoI and we have Senior Citizens coming into the office wanting to close their a/c's because of what they hear on Joe Duffy etc. As Golden Years customers they do not pay Fees. Neither do students. Anyone who has never used 365 Online/Phone will not have any changes whatsoever. If you're already a 365 user you will easily know how to circumvent these charges. It may mean making a few more transfers, topping up your phone or whatever, but it's not rocket science!