Ok, here's the thing. They were in contempt of court for refusing to undertake not to interfere with a governmentally approved project. And they were jailed for it, because they broke the law, it's that simple. They are in jail for breaking the law, not for protesting.

Now that said, I don't agree with the terms of contact agreed with Shell, they're a relic of previous decades when governments were bending over backwards to get any kind of inward investment just to get people off the dole queue. Nowadays, especially in the oil market, with demand being so high, it's the governements who have the companies over the barrel but some little bureacrat in Dublin decided it was too much to draw up a new contract and just handed out a near carbon copy of one from the 70-80s.
However, it's good to hear that the Danish government (a new left wing alliance I beleive) is taking an interest in the issue and a representative from the Irish labour party has received promises that it will be raised in the parliament by the Danish Labour party.