FLT stands for "faster-than-light travel" specifically, while FTL is used in other sentences involving "faster-than-light", like FTL drive, or even FTL travel.
I've really never (until this thread, at least) seen FLT used instead of FTL travel. Usually, the context is clear enough that the "travel" part can be omitted anyway.
I posted this in the comments at Eric Raymond's blog:
Then I realized some here may find it useful.
Extensive use of abbreviations and acronyms was primarily a convenience for writers, when writing was done by hand and then by typewriter, there is less justification for it now when most writing is done by computer. And as my comment points out it is usually a negative for readers. It does benefit readers when you can convert a long phrase into a readable word, SCUBA and LASER spring to mind, but that doesn't occur often.