It would be very strange for a manager to pick on one player and ignore the others who have played GAA, so I don't think that could be the point of contention.
As a manager Mike is expected to be above personal pettiness, and therefore I think it unlikely that there is a personal issue at play here.
Perhaps Eoin's extended run on the bench is simply Mike placing faith in Conor Molam (who, with the exception of a couple of recent games has had an excellent season to date).
Perhaps Eoin is finding no joy in playing soccer with Limerick FC? Maybe he just fells that his heart isn't in it anymore. Things are looking dismal off the pitch and maybe he doesn't see any light at the end of the tunnel?
Hopefully the Monaghan match will provide some much needed answers.