I've done online check in each time except for the last trip. The only reason I didn't do the online last time was because we were a Grand Gathering and had one very special room request for my wheelchair bound father and we had four rooms in total. I regretted that decision when I walked in and saw the entire check in line queue totally filled. Took us a half hour to get to the front of that line so never again.
I don't have any room requests and we usually will arrive before noon so I've always had the room ready when we do the online check in. If you have any problems, it's not like you are not visiting with a human being - there will be a Cast Member checking you in.
To me, doing the online check in is much better than having requests and doing the regular line. I'm not that picky on where my room is located.