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To me there is a big difference between saying "all Muslims are secretly terrorists" and saying "the Quran is a fictional book full of bad ideas" most atheists argue the latter because we all have religious loved ones in our lives and we know they aren't secretly genocidal, we just want them to look at the world more rationally. 
Maybe you or the OP would argue "you only think these are bad ideas because you are judging by modern standards". My counterpoint is simply, God isn't bound by standards of the time, an all powerful omnipotent being can't justify bad ideas by saying they were acceptable by the standards of the time.
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With religions as big as the ones you mentioned, you're talking about hundreds of millions of people, all with different personal beliefs and different levels of acceptance of the different teachings of their respective religions. So most generalizations are just gonna be false.
That being said, there are identifiable issues that are rooted in religious beliefs that, even though we're not talking about 100% of them, a large proportion, sometimes a majority, accept them as they are thought, or as they are written in their respective scriptures. I think it is fair to criticize and "scrutinize" these issues, not because they are rooted in texts written so long ago, but because so many of these people accept them and live by them today. >


I think it is fair to criticize and "scrutinize" these issues

Of course it is fair to scrutinize the issues. I am speaking the effectiveness of scrutinizing the religion as a whole. >


While the scriptures may contain writing that is callous towards women and gay people, it is important to remember that the bible and Quran were written at a time when values and morals were vastly different and these groups were viewed and treated much differently than they are now.

And if we treated the books merely as historical texts then you might have a point.  Looking at a piece of literature within the context of the time it was written makes sense for literary critique - for example, talking about how the language in Huckleberry Finn was the common language of the time and not putting too much critique of that in your review.
The problem arises that religious texts are not used simply as historical documents; they are used by many as guides on how to behave in the modern world.  Those passages of scripture are quoted by many as how one should believe and behave today and used as a moral rubric for decisions in 2023.
That is something that should be scrutinized and critiqued in society.  Any moral framework, regardless of when it was written, is fair game for discussion when people are attempting to justify that framework's modern-day use. >

That response is entirely divorced from how people do this in practice. When people scrutinize religious texts in order to criticize and critique religious people, they're not looking for passages that are widely quoted and deployed by religious people to support moral frameworks they disagree with in order to discount those moral frameworks. Doing so would be pointless, because if you already disagree with the moral framework that is based on the text, well it doesn't really matter what the text says, you can just disagree with the end product - the moral framework that is being applied and used in the real world - rather than the text that it is allegedly based on. The authority of the Ayatollah is theoretically derived from scripture, for example, but you don't see a lot of people going to scripture to discredit him, because dictatorship is already a thing that everyone disagrees with. You can just criticize the thing, the textual support for the thing is irrelevant
In practice, scripture is scrutinized for purposes of critique by looking for passages that mainstream believers either ignore or interpret in a non-literal way, in order to make them look bad. So you go and find the sword verse for example, which most modern Muslims interpret as having referred to a specific time and not as a duty for all Muslims to carry out, and argue that no, they're actually wrong about their own religion, and this verse proves that Islam is not a religion of peace, or whatever. In the process, the critic of Islam becomes an amateur Islamic theologian, doing their own hermeneutics to invent their very own Islam which they can then criticize. It's not a very productive activity for criticizing how the text is used to justify a modern day moral framework, because in order to do it, you have to ignore the modern day moral frameworks and just make up your own one based on how you think the text ought to be interpreted. 
Essentially what you're saying is that people should criticize scripture in order to criticize people who have bad morals based on that scripture, but in practice what people actually do is use scripture to criticize people who have good morals based on that scripture. Because obviously bad morals can just be criticized on their own. Nobody goes to the Qur'an to prove that terrorists are bad, because everyone already agreed that terrorists were bad without having read the Qu'ran. What people do instead is go to the Qur'an to prove that peaceful Muslims are secretly terrorists.