Note that Java compares very favorably with C. (Of course, the real thing to take away from that chart is: why don't all the JVM users switch to Haskell? It's more concise, safer, and has a better community.)
If you read the methodology listed in their FAQ, they state in bold - "Time measurements include program startup time".
http://shootout.alioth.debian.org/help.php#time
If you read the section "What about Java?" they mention ADDITIONAL measurements, which are only shown on the Help page, and indicate how little difference JVM startup time makes once these programs have run for 5 seconds and 20 seconds.