Jeff makes some excellent points about travelling with a bike both on the airlines and on the cattle transporter. I'd like to add to these.
For first timers, the cattle trucks are two level trailers cleaned out for the transport. By packaging your bike as suggested by others, you won't have any problems. Be aware though that taking your bike onto the truck can be hazardous especially if its wet and you have cleats on your shoes. The cattle truck ramps have ribs welded onto them for cattle hooves but they don't come with handrails. A good collaborative effort is required to help each other up and down the ramps. Don't be afraid to ask others for help as it can be dangerous trying to balance yourself and bike. There is also not enough head height on the lower deck, so it requires good help passing the bikes in. Some of the bike packaging done by zealous owners mean the wheels don't turn, so the bike has to be lifted up. I have seen one unfortunate persons holiday end before it started with a nasty fall on the ramp.
I make a point of getting up on the truck and chipping in with the loading and unloading. At least I know that my bike has been well stacked and the same for the bikes either side. I also know where to find it at the other end. I've found the truck drivers to be excellent and the ones I've dealt with really worked hard getting the truck loaded promptly and safely. I don't appreciate the people who wait for their bike to be unloaded and clear off. If everyone chips in the work is over in no time, safely and efficiently.
Pedals are best removed from the bike as they get stuck in other wheels and are a main cause of scratches. Take any clip on stuff off the bike like lights, bags etc. Don't leave pedal removal until the last minute. If they haven't been off in a while they can be very difficult to remove especially without a pedal wrench. Get you bike shop to slacken them for you.
A point to note for first timers is that when the bike is unloaded at the start you have to be able to assemble the bike and ride it there and then. So you need to have what is required to ride the bike. Helmet, shoes, water bottle and any tool you need to assemble. Its no good taking a large bag of stuff and then wondering what to do with it when the bike is assembled and you have to ride to the first nights camp spot. Everyone chips in to help get the bikes ready so anyone who needs help should just ask. BV explains this in the pre-ride advice.
I can only reiterate what Jeff says about the spacers for the frame when flying with your bike. These plastic spacers in place of your axle prevent the frame from crushing. If you can't get them make them out of wood or plastic or use some old hubs.
Provided the bike and box do not weigh more than 32 kgs you can use your sleeping bag or sleeping mat to pad the bike. I wrap newspaper around the oily bits first, then place the sleeping bag over the frame etc. Newspaper is an excellent degradable packaging easily available. If you wrap the sheets of newspaper around the tubes of your frame, it provides excellent protection.