The Institute for Creation Research must be Isaac Newton’s biggest fans. Why else would the thrice-weekly-pseudoscientific-report-on-last-fortnight’s-news (on average – this is from last month) for Friday the 23rd be called Israeli Library Digitizes Newton’s Theological Works? Why else would they care?
Mr Thomas says (skipping into the middle of his article):
Modern physics textbooks teach Newton’s laws of motion, but students are not generally exposed to his prescription for truth discovery. Why have secularized, modern cultures emphasized and valued Newton’s scientific contributions, yet downplayed and devalued his theological contributions?
I suspect that it’s a similar reason as why people downplay his work on alchemy. Newton was a heretic, he did not believe in the trinity; nor the immortal soul; he liked bible codes; and he chose a number of dates for the end of the world (which expire around now, as it happens). In other words, this aspect of his work is embarrassing. You’ll note that the ICR, too, do not bother to mention what he actually believed.
Milka Levy-Rubin of the Hebrew University of Jerusalem’s Department of History told the Associated Press:
Today, we tend to make a distinction between science and faith, but to Newton it was all part of the same world. He believed that careful study of holy texts was a type of science, that if analyzed correctly could predict what was to come.
If Newton was able to study both science and the Bible without conflicts, then why should anyone frown upon scientists who do the same today?
The link for that quote is here. Generally we have good reason when we “frown upon” scientists who go code-hunting in the Bible, but that’s not what Mr Thomas meant.
God is a rational being, and thus one should one expect His creation to reflect His rationality and His intelligent creatures to comprehend what He has made.
Ha! You get the picture. Read the rest yourself. Or, if you prefer, you can read the works of Newton here. But I’m not forcing you to do either.
Eye on the ICR 
I’d say a pretty big reason why his theological works are devalued (other than the embarrassment you mentioned) is because they possess little value anyway. We teach his laws of motion and can send probes into space with them.
Whilst I haven’t read his readings so can’t say for sure, I’m pretty certain you couldn’t do astronomical calculations based off them, or figure out why apples fall by spending a great deal of time pondering a deity.
Society, to put it bluntly, doesn’t give a shit about theological works because they aren’t especially useful. Science is.