FreeGLUT is a simplicistic framework for the creation of small OpenGL demos. Alternatives to FreeGLUT would be SDL, GLFW, or full blown frameworks like Qt.
Mesa is a open source implementation of the OpenGL API, and together with the DRI/DRM project drivers forms a full HW accelerated OpenGL implementation. If you're using Linux and use your GPU with open source drivers, Mesa is the OpenGL implementation you use. That's not a choice, that's a fact.
They're completely different things and neither can replace the other.