From the BBC yesterday:
There has been a history of tension between the secularist military and the governing AK party, with the two sides engaged in a war of words for the past two years over allegations that parts of the military had been plotting a coup.

Investigations into those allegations, known as the "Sledgehammer" conspiracy - appear to be the root cause of today's resignations, says the BBC's correspondent in Istanbul, with the senior military wanting to go ahead with scheduled annual promotions for some of the officers implicated - and the government refusing.
Link:http://www.bbc.co.uk/news/world-europe-14346325

When this subject has come up before it has been unclear if the prosecutions are substantiated by evidence or an attempt by the government to undermine the military's role as 'guardian' within Ataturk's principles.