The short answer: Yes.
The long answer: Yes, but their vote may not get counted. Absentee ballot requirements vary from state to state (for instance, some require a witness to sign a form), and given the number of absentee ballots a lot of states are having to send overseas to troops, this complicates things. Some states were not prepared and have not necessarily allowed for the needed turnaround time that sending a ballot over there and back again requires.
Have you had your head buried in the sand for the last few weeks? There have been a few stories out there in the news about troops voting, namely saying that there were a number of difficulties in 2004 and only about 30% of the troop vote was counted, and that they expect similar difficulties this time around.
Here is an article from CNN that explains what's going on:
Ballots from U.S. troops risk being discarded - CNN.com