Hi
Yes you can. I do it all the time. The only thing you should take care of is when you open one marker cap, open the other end just to equalize the pressure evenly into the barrel of the marker. Also I put the markers I used in the plane into a separate ziplock bag to know which one I used an I do the same thing when I reuse them on the ground so you do not have to open them all and that is to re equalize the pressure otherwise you may get drops of ink all over. I have learned the hard way... ;)
You can get more info on traveling by plane with copics on CardCreme blog:
http://sherrie-cardcreme.blogspot.com
Sandra