Well, there are a few issues involved with a book like the Bible.
1) It was written in another language and across cultural contexts, meaning that just reading might not get the intended message, which would have been more apparent in the original language and context.
2) The purpose of the Bible is clearly not to be a textbook, although, I will admit that a textbook would make things easier in some ways. Instead, it is a collection of stories and writings that were considered to be inspired and beneficial to read. Because it is not a textbook though, there are issues of rhetoric involved, as the Bible clearly enjoys the use of forceful overstatement, and there are issues where narrative is used but wouldn't necessarily make sense without recognition of the purposes of it.
3) The Bible wasn't even necessarily written to be clear, as it has to be remembered that parables were used by Jesus for the purpose of actually being somewhat more difficult, so that understanding would be the reward for diligence.
So, I would only claim Ingersoll's point to be absolutely valid if the following things are true:
1) The obfuscation of meaning isn't an effort to drive people to push deeper. This could be used as a test of diligence and mystical readings tend not to be straight-forward to provide a mystical experience.
2) Interpretation of the text is much worse than it could be from a text of this kind of cultural and linguistic background, and that is written in a narrative structure. AKA, it must be shown that the text obfuscates things when there is no other explanatory factor.
Some evidence for this kind of a point though is clearly the fact that large divisions in Biblical teaching have occurred over history, and the large theological changes that have occurred over time, so Ingersoll's skepticism cannot be outright dismissed, as it is not the misreading of atheists that seems problematic, but rather the interpretation issues between various Christians about central doctrines.