When we call source activate ... it starts a Python virtual environment. The purpose of a virtual environment is to created an isolated Python set-up. So it is by intention that the Python packages you have installed at other places outside that virtual environment are not accessible from within it. I would except fenics to install matplotlib as a dependency but in any case you try to explicitly install it.
Your error message says that matplotlib is already installed in /usr/local/lib/python3.6/site-packages which means you are calling pip3 install matplotlib from a terminal where fenicsproject environment is not yet activated.
If you are trying to install matplotlib in the same environment as fenics try
conda install -n fenicsproject matplotlib