When Amara was overpowered by Crowley, even though she was still recovering from her imprisonment at the time, many users whined about how she was "so weak" and how she was no threat, yadda yadda. Now that she overpowered God (which was already stated to be possible, if not likely) after catching him off-guard, everyone is whining about how Chuck is so weak.
Neither of them are weak. Chuck was attempting to lock her up, which required him to take the Mark from her - a considerable effort all in itself, given that she is more powerful than he is. Naturally, she freaked out and fought back (note how she had initially surrendered), which caught him off-guard and while he was already exerting his power (remember, God is not omnipotent, so he can't just snap his fingers and make stuff happen - it takes effort in his behalf to get things done).
Amara was always said to be able to kill God, and the fact that it took four archangels to, and I quote, "barely" lock her up, also implied she was superior to him in power. God wanted to surrender to her, rather than fight, because he knew he couldn't win.
If you didn't see this as a possibility, it's your own fault for conflating God with God and expecting a "finger-snapping, all-powerful creator", rather than the entity that's been presented to us since his first appearance: a fallible, human-like god.
EDIT: Oh, and let's not forget that while everyone was focusing on God being overpowered by a more powerful being (which is the logic equivalent of 1=1), they're forgetting his creation of an entire universe, plus Heaven, Hell, and Purgatory, resurrecting an entire town, healing their wounds, curing the Rabids, and getting rid of the fog instantaneously, being in two places at the same time, separating a soul from whatever had it anchored to Earth and sending it to Heaven, and so on.
God is powerful. He's just not the most powerful.