With aerating the shape and layout of the lawn matters more than size. Lots of stuff to go around equals hard work, while a larger wide open lawn is pretty easy. I agree: NEVER charge by the hour. Have an hourly rate in your head that you hope to make (I try for $60 mowing, and $90ish aerating) and use that to set your bid - but don't talk to the customer in these terms. They will always feel that that is way too much. They instantly forget about equipment costs, maintenance costs, bidding/driving time, and on and on and on.
As far as flagging sprinkler heads, I don't do it either. For my own customers I aerate after mowing and I can usually see all the heads, for the one time customers that call, I ask that they have the lawn mowed before I come out. If you do mark the heads for them you are going to be spending a lot of extra time and even then it is easy to miss one. I have aerated a lot of lawns and I've never got a call back that a sprinkler was broken. Maybe it has happened but I'm guessing the customer realized that when they hire someone to roll equipment like that around on their property there is potentially some hazard. If I did get a call back to fix a sprinkler I would happily take care of it for them and then just make a note to insist they mark their own heads before I came out the next time. Knock on wood - so far it hasn't been an issue.
Lastly, if I'm aerating a bunch of lawns in a day with a helper, I try to split the operating time with him. It is HARD work, and feel like asking him to run a machine like that for 8 hours a day isn't fair. If you are by yourself I wouldn't schedule more than 3 to 5 of them in a day.