Why do basketball players make more than school teachers?
F/J can be justified two ways.
1. Employee is well-rested and productive from the moment s/he hits the ground until the minute of departure. This includes everything from check-in to security to arrivals formalities, lounge for a shower, and the like. This is not simply a calculation as to what an employee makes per hour, but of the productive use of their time. Somebody who is asleep in their hotel when they could be at work means there are that many business tasks accomplished in the time the employee is out of the office.
2. As to employee comvenience, it's a competetive market. All things being equal, a regular long-haul traveler who is also high-performing will opt for the job with the better perks. That leaves your company with the non-performers. Having said this, the operative words are "all things being equal." Would somebody leave over F/J travel if it meant a $50K pay cut? Not likely. But, just like all perks, premium travel factors into the employee's decision-making process.
There is no cookie cutter answer to this question. At a cash-strapped startup, premium travel may not be doable even if it seems like a great idea. Cash flush mature company with a competitor breathing down your neck and it's time to shell out.