Alas, auto-farming flax seems to be difficult, if not impossible.
You can make it semi-automatic quite cheaply. Here is my trial netherwart farm in building (for GT methane): http://imgur.com/a/GgE0i (transposers below are collecting nether wart). Basically you are planting by using seed bags in deployer. You will need replenish seedbags eventually but one deployer full of full seedbags will be enough for 216 cycles. Just add a timer calibrated to flax growth rate and you are good to go. Of course you can always make small autofarm using bonemeal.