Like you, I also prefer to show my passport since that only means wrangling one document instead of two. About 50% of the time, I have the same type of experience that you describe. I'll caution you not to be eager to attribute this to malice, as it tends to be (at least in my experiences) merely a symptom of a poorly-planned process.
One time when I was having this problem, I was on the same side of the desk as the HR rep and I could watch what he was doing on the computer. The process that he was following included steps for "photocopy drivers license" and "photocopy social security card", and the form had places to attach those copies. He had to dig around for about 10 minutes to find an older, "alternate" version of the form that asked for the passport instead of the other two documents. He told me that practically everyone he sees uses their drivers license/ID and social security card, and he only sees one or two passports a year (most Americans don't even have one). For that reason, he never can remember the process for using passports and has to look it up every time.
The law says that they have to accept a passport alone for your I-9, but the process for doing so might be more complicated than the more common cases. Your manager may simply not know how to process that or doesn't want to jump through the extra hoops to do so, and is instead trying to steer you towards the more common case that they're comfortable with. I suspect that you'd have similar issues if you tried to use one of the other uncommon forms of ID like a Native American tribal document, or a form FS-240 (used to document a US citizen that was born abroad). I've even known people that had problems when using drivers licenses when those licenses were issued by a different state.
Also, don't forget that passports have lots of anti-counterfeiting measures, many of which mean that they don't photocopy well at all. On a cheap copy machine, the photo may not even be recognizable. Some companies keep copies of your photo ID in your personnel file. If they're unable to make a serviceable copy of your passport, they might reasonably ask if you have a different ID they could use. That would be an internal company policy and not part of the I-9 process, though.