The rationale comes from concern about identity theft. I would guess that IT departments in some airlines are not *that* concerned about the security of the passport details of their passengers - they'll follow standard procedures but are unlikely to make strenuous efforts over it. When a company is known to be handling the identity details of over 1 million people and subsequently retransmitting this data on to various Govt bodies, it becomes something of a target for hackers and rather dubious groups.
I agree that I am unlikely to be affected, but more than once identity details under the care of Govt and companies have somehow leaked out. When this refers to a highly trusted document like a passport (as opposed to just a phone number), the potential for identity theft becomes much larger.
Plenty of companies will give assurances about how secure your details are. It's not possible for the average individual to verify these claims in any meaningful way. Furthermore, where data has leaked, the organisation has typically give great assurances about the security of people's personal details !
Take the risk enough times, and someone will start to impersonate me