Why did Tommen Baratheon stop his mother from attending the funeral of Myrcella in Game of Thrones S06E02? What was the point of that? He said he doesn't want to lose his mother again, but how did this decision help?
The High Sparrow made two things clear.
That Cersei was not done. She only confessed some crimes, not all that she was accused of. She was released pending her full trial, in s05e10 "Mother's Mercy".
SPARROW: Good. But these are terrible charges. And the realm must know the truth of them. If Your Grace has given honest testimony, your trial will prove your innocence.
CERSEI: Trial? I have confessed!
SPARROW: To a single sin. Others you have denied. Your trial will separate the truths from the falsehoods.
CERSEI: I bow to the wisdom of your High Holiness. But if I might beg for just one drop of the Mother’s mercy. I haven’t seen my son... I don’t know how long it’s been. I need to see him. Please.
SPARROW: You have taken the first step on a path back to righteousness. In light of this, I will permit you to return to the Red Keep.
Off screen on s06e02 "Home", he (or one of the Faith Militants) made it clear to Tommen that Cersei would not be allowed into the Great Sept of Baelor (The Church/Holy Ground). This came with an implied threat of force if Cersei would try. Like every other time, Tommen had to make a choice of ordering a fight between the King's army and the Faith or backing down, and once again he backs down.
JAIME: Then why didn’t you let her come? She has every right to be here.
TOMMEN: They told me she wouldn’t be allowed in the sept. If she had tried --
JAIME: They’re not putting your mother in a cell ever again. Not while I’m here. Why haven’t you gone to see her? Everything she endured, she did it for you.
He keeps Cersei from going to prevent that fight, and from letting them take her again. The Sparrows have no problem forcing the issue with blood if needed, but Tommen won't. So it helps by preventing an unneeded bloodshed.
He explains it to Jaime right after the scene with the Zombie Mountain. He is scared that the High Sparrow will jail his mother again; he is scared of losing her a second time. He felt powerless when she was taken from him, and now he seems to be turning out just like his past brother, ruthless and cruel. As he explained to his mother, he should have slaughtered everyone who was responsible for her jail time. He didn't do it and regrets it.
As for how it helped, it didn't. It simply showed the viewers how Tommen felt about his mother's jail time. He is scared to lose her and is ready to jail her himself if it prevents the High Sparrow from taking her again.
My final answer is that Tommen was weak and insecure. He can't do anything to the High Sparrow, so to prevent any further conflict with him, he makes her unreachable.