Just to share an experience, I hope that it is useful as this cost me precisely nothing and ended up skipping all the horrible queues.
I flew a bike from London to Bali recently.
It was a reasonably good carbon fibre model and was a bit concerned that I would end up with a pile a dust and a few components.
1. Went to the very helpful Chelsea Bikes 427 King's Rd, Chelsea, London SW10 0LR. They gave me a packaging box for a recently delivered new bike. Thanks guys.
2. Packing process.... Followed from the many sites that have tips and ideas search them there are many. Saves me repeating them all here. One thing I did in addition was to pack all the empty spaces with another broken down box to make sure the contents didn't slide about. Use a two litre coke bottle cut in half to put over the derailleur arm packed with extra paper. Packing process takes about 2-3 hrs.
3. Once packed read your airlines policy. You'll find that you don't understand it any more than I did. I tried to book the bike online in advance and found I couldn't. Still don't know why.
4. Gave up and took it to the airport. The box for a bike comes up at about 150cms. This fits in the back of most estates and will slide into the folding seat space leaving one or two of the back seats available. We had a Vito van so no problem at all. Despite the misgivings of the driver.
5. Airport.... This was the good bit, there were enormous queues for the bag drop, as usual. Makes me wonder why they bother with online check-in at all. So looked around and found a desk for overweight baggage. No queue. Spoke to the very helpful person Paul on the desk. He took the time to look at our flights, connections and timings. He then weighed the backpack, worked out that the bike box could fly for free as the connection flight had better baggage allowances and we were able to use those from the off. Fab. (For info the bike packed in a box with a lot of extra bits in the box weighed in at 20.1Kg)
6. Arrived at Bali having changed at a major middle east flight hub. Box with bike came out first. In perfect condition, unsquashed and looking exactly as it had when I dropped it off.
7. Bike survived. Only problem where to store the box while you move about. Don't worry someone here will help you as that's what happens. They do lovely and helpful is built in.
8. Moral of the story GO TO BALI. Don't bring the bike it's too hot as you can rent one with a motor for next to nothing.
9. Shared so you can see how easy it is to fly. Having read a lot of the online content it's seems that Air carriage policy changes all the time.

Good luck and take you bike round the world with you. It used to be like that for ski equipment so eventually they cottoned on to the money making potential so take the bike for free while you still can.
Ric

If you scroll right down to the bottom of this link, I talk about Rowan's and my experiences flying out of Heathrow in 2012.

Charlene Barach (Machka) - 2012 Round the World Tour


As for Bali ... well ... um ...

I live in Bali. Rental bikes tend to be clunkers. Nothing I'd care to ride. I only know of one place where decent bikes can be rented. Plenty of good riding. Away from where tourists and traffic congregate, of course. Great place for credit-card touring.

Deceptive thread title. I was expecting this:

I've only flown with bikes once, but I didn't find the baggage handlers to be the brutes that everyone expects. Nothing out of the ordinary on the boxes, only one little hole poked in the side of one.

Reading airline policies is key. One required me to actually call the reservation center and book a space, or risk showing up and there not being room on the plane. Check in agents on both ends were friendly and helpful. The head agent for Brussels Airlines was also a cyclist, and ushered us through the VIP line. The gate agent for Air Canada conveniently forgot to charge us our $50 fees

As to why there is online check in: for those of us who generally travel carry on only.