I'm just not a fan of online checkin in general. I only do it now when it means for me getting on the waiting list for FC earlier. If I have been upgraded or F is already full, I don't online check. This was the case with my flight on Thurs...F was full so there was no reason to use my time and printer to print out a boarding pass (all the time trying to remember to check some box so it wouldn't print out a bunch of cr*p ads). Since I am a 'miles whore', I used to do it when they bribed us with bonus miles...I stopped when they took the bonus away.
I am not sure that I believe them when they say that online checkin won't cause added complications should I get a flat on the way to the airport or some other mishap that would cause me to be late and miss a flight.
Since I am not a big fan of online checkin in general, I am even less of a fan of it being done for me automatically by Big Brother Continental. I find this very heavy handed on their part.