I recommend removing the disc rotors when you travel with a bike regardless of the packaging method.
I have a hard sided case and have done the cardboard box thing
(my fat bike does not fit in my hard sided case).
Hard sided cases rely on compression to keep everything in place; compression against the flat side of a rotor is not a good thing.
Remove the rotors and pack them on each side of a piece of rigid material that will reinforce them and tape the whole thing up.
They can be easily put back on with the proper Torx wrench.
If this seems like overkill, keep in mind TSA WILL unpack your bike.
Do not bother closing a cardboard box before getting to the airport, because they will just cut it open.
I leave the box open and leave a roll of tape on top for them to seal it with.
I pack any loose items in the box with the understanding that they will be removed and likely reinserted in a different spot inside the box/case.
That being the case, you want loose items padded or enclosed in something for when they end up someplace you didn't intend them.
I usually make sure to take all the same tools I used to disassemble the bike and pack them as well (usually in a separate padded bag) in the same box/container.
I have always favored the center lock rotors because they were easier on and off for travel.
bicycles.stackexchange.com/users/13710/Deleted User
I have flown 6x with my bike (Cyclocross Disc) in a soft padded bike bag and never once had issues with the rotors.
Numerous other MTB friends never remove the rotors either and have not had trouble when flying.
Echoing the comment by @Daniel
, I'd be more focussed on the dropouts and RD and making sure those are supported.
You are way more at risk stripping / losing screws than bending a disc.
The wheels will be double padded by the wheel bag and the bike bag.
bicycles.stackexchange.com/users/10723/sjakubowski
A torque wrench is definitely recommended, but some people develop a "feel" for the correct torque.
There is usually blue threadlocker compound on the screws.
There are small, cheap simple "flexion" torque keys that do the job quite well.
My MTB came with one, actually.
bicycles.stackexchange.com/users/23382/B00g
A few years late,
but I thought I'd share my two cents
- I recently flew with my mountain bike in an EVOC bike bag, and my front rotor did actually get bent out of shape beyond repair (according the local bike shop).
So, I would recommend always removing the rotors.
bicycles.stackexchange.com/users/20811/user1515657
Since posting this question I went on a tour for a few months which involved flying with my bike twice.
Both times it was packed in a cardboard bike box from a bike shop.
It may have been unclear in my original question, but my question was specifically about the disc rotors, not how to pack a bike in general.
When searching elsewhere
I found there was lots of info about general bike packing, e.g. remove the rear derailleur
wrap it in padding, use a dummy axle for the fork, etc, but I didn't find a lot of info on disc brakes.
Anyway, to be safe I removed the rotors, interleaved them with sheets of clean paper towel to avoid contamination (so three sheets total), then sandwiched them between two squares of press-board, which I then wrapped with duct tape.
This may indeed be overkill
but I'm sure it can't hurt.
To keep the torx screws safe, I put them back in the holes they go in and screwed them in a few rotations.
When I put the brakes back on I did not use any special alignment tool or torque wrench, I just used the torx driver on my multi-tool and put them in by hand.
bicycles.stackexchange.com/users/11416/SSilk
The thing ive found an issue isn't the rotors but actually the headset/stem (especially an integrated one piece setup) being the issue.
My friend has a Specialized Venge Vias (disc) and he obviously had to remove the headset to turn the bars to fit into the rigid bike case.
Removing the bar/stem means that there's no spare cable/hose
so he had to
have the brakes bled then re cabled when he arrived there and the same when he got back as they dont like being taken apart.
an expensive trip just to take a disc braked bike.
bicycles.stackexchange.com/users/38778/Gareth
I've been looking at a few tutorials on packing a bike to take it on a plane, and most of them make no mention of disc brakes. One did specifically mention disc brakes, and recommended taking the rotors off and sandwiching them between two small sheets of plywood to stop them getting bent or warped.   Any thoughts on this?   Can you just put them back on with the allen key bolts that attach them? Or do you need special alignment tools and a torque wrench?
Should disc brake rotors be removed when packing bike for travel?
bicycles.stackexchange.com
<disc-brake><transportation>
bicycles.stackexchange.com/questions/31097
bicycles.stackexchange.com/users/11416/SSilk
Most people recommend removing the disc rotors before taking a bike on a plane as there is a riscK of them getting bent. However, others have flown with the bike intact and had no issues. General consensus is that they should be packed in a protective bag as should all loose items, like screws, that may get lost and the tools needed to replace them.  Some commenters suggest that the bike bag will provide enough protection without removing the rotors, but others disagree and recommend reinforcing, padding and storing them separately. A torque wrench should be used to disassemble the components, and the tools can be packed along with the bike for later assembly.
Some commenters suggest that the bike bag will provide enough protection without removing the rotors, but others disagree and recommend reinforcing, padding and storing them separately. A torque wrench should be used to disassemble the components, and the tools can be packed along with the bike for later assembly.