I have done it both ways and can see folly brewing either way. That is why it is very important to have in your contract - a few items of interest.
1. Kill fee - if the shoot gets booked, the airline and travel expenses paid for by me, then those fees are automatically due should the shoot be canceled. This is in addition to any non refundable booking fees (notice I don't use the term deposit)
2. If the client does not have the ability to pay for travel in advance at the time of booking then at least 50% is due at the time the contract is signed. I can and will float 50% travel costs under most circumstances - but I charge an additional fee for doing this too. Credit is NOT free.
3. I try to book my own travel arrangments. If in the US it easier. But several times in my career I have traveled outside the US so international travel with several $$$$ worth of gear, means that I want total control. I do shoot for clients that actually have travel departments either off site or onsite, so they do sometimes insist that I use them. But so far that has always garnered some great flights.
4. Consider shipping the camera or studio gear via Fed-ex or other shipper, this will often reduce the chance of lost gear, lower the prices (no weight limit for the bags) and best of all they will be at your destination when you arrive. No hauling crap through the airport. BUT backups are required so plan accordingly.
5. Make sure that you charge lower portion of your creative fee for the time spent traveling, you get paid for that time too.
6. Lastly, and I cannot stress this enough, make sure that you have cold hard cash to handle any emergencies that may arise. Sometimes credit cards or debit cards cannot be used. Get receipts for everything, and keep them handy. Missed airplanes, dead rental cars, lost gear, and even sickness are always an issue lurking in the bushes. I always try to plan for the absurd, and more than once have had to use it...
My best friend just had to replace his entire laptop kit when it was stolen out of his car. He went right to Fry's got the same model, bought the software and had it up and running 4 hours prior to the wedding flight down to Jamaica. He was able to complete the shoot and present the couple with the required slideshow of the nuptials as per the contract. WHEW.

