Scripture commands and condones the indefensible.
The objection, in full
Slavery regulated rather than abolished (Lev. 25, Eph. 6). Herem warfare in Joshua. The Midianite massacre (Num. 31). Bears mauling children for mocking a prophet. Contradictions between Gospel accounts of the resurrection morning, the genealogies, the death of Judas. If this is a divinely authored book, the author has a great deal to answer for; if it isn't, the case collapses.
The God of the Old Testament is arguably the most unpleasant character in all fiction.
or, in plain terms —The Bible says some pretty awful stuff. How can it be the word of a good God?
If a passage seems to contradict charity, you have misread it.
I will say this plainly, because it is the rule by which I read Scripture and by which I urge every Christian to read it: whoever takes from the divine writings a meaning that builds up love of God and neighbor has not yet been deceived, even if his interpretation is not what the human author intended. But whoever takes a meaning that contradicts charity has misunderstood, no matter how literally he reads.
The hard passages — the conquests, the imprecations, the laws we now find barbaric — were written into a particular people at a particular stage of moral formation. God accommodates himself to the capacities of his hearers, as a father speaks differently to a child than to a man. To read these passages flatly, as if they were timeless commands rather than steps in a long pedagogy, is to read them as the literalist and the atheist both read them: badly.
The trajectory of Scripture is from the herem to the Sermon on the Mount. The atheist who quotes Numbers against the Gospel must explain why Scripture itself moves in the direction it does.