GCC 4.4 includes support for processor features like SSSE3, SSE4.1, SSE4.2, and more that are not present in GCC 4.2 (which is used by FreeBSD.)
Due to licensing issues, the newer GCC can't be used in the base OS.
The performer of this benchmark didn't say they compiled everything with GCC 4.4 for a apples to apples test.
The documentation for compiling things with GCC 4.4 are here:
If you want an honest test where it is proved Ubuntu is faster, you should perform a fair test. If you wish to "just show FreeBSD slower" that can be done by running the benchmark in an unfair way. Like was done by this test.