I do online check in all the time and haven't had a bad room location yet. In fact, I've stayed at BWV twice since doing online check in, and had rooms close the elevator both times, whereas before online check in I did end up at the FAR end of the hall twice. I'm not saying one is better than the other - that's just how the dice have fallen for me.
The goal with online check in is to get you into a room as close to your arrival time as possible. So if you are arriving early in the day during a busy time, it could be that the only unoccupied rooms when you arrive are farther away from everything. I'm usually checking in after work, right around 4:30, so maybe that means they have a larger pool of rooms to pick from when assigning mine. I usually don't have room requests because I'm not too picky, and so far I've had great rooms.
It does save a lot of time, unless you get someone in the online queue who wants to change rooms or has a lot of questions. That holds up the line substantially. I always say if you have a request that is going to make or break your trip, don't do online check in. Check in at the front desk so the CM can go over the available inventory with you and pick the best room to meet your needs.