This is a very good, free program.
It works with AS3.0, has all the features you would want, and is well-documented. Further, it works on a large number of languages, not just AS3. I have not tried using it on Flex programs, but it did identify and count the HTML file which happened to be in my directory. It also noted in the output that it was HTML, and not AS3, so I could ignore that set of lines if needed.

Windows command-line based, but don’t let that discourage you. Here is the BAT file setup I am using to count AS3 code:

REM =====================

echo off

REM set variables
set ASDir=C:\root\directory\of\your\AS3\code\

REM run the program
REM See docs for different output formats.

cloc-1.09.exe --by-file-by-lang --force-lang="ActionScript",as --exclude_dir=.svn --ignored=ignoredFiles.txt --report-file=totalLOC.txt %ASDir% 

REM show the output

REM end

REM =====================

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