Finally got netperf and flent working on Raspberry Pi, thanks Toke to pushing me in the right direction of manual compilation.

Here are the steps to get netperf and flent working of latest clean Rasbian install:

   $ sudo apt install autotools-dev automake

   $ git clone https://github.com/HewlettPackard/netperf.git

   $ cd netperf

   $ ./autogen.sh

   $ ./configure --enable-demo

   $ make

   $ sudo make install

   $ sudo pip install flent

And that is it :)