Manus himself held no prejudice against Squibs; his confusion was entirely due to his inability to understand Dumbledore's decision.
Making a Squib the caretaker of Hogwarts—even setting aside the widespread, deeply ingrained discrimination against Squibs in the Wizarding World—was hardly a cushy job for that Squib.
It could not even be called a normal job.
Although the former caretaker, Pringle, had barely interacted with Manus, he still knew something about the caretaker's duties.
The Hogwarts caretaker was primarily responsible for maintaining order and security at the school. To that end, the caretaker had to handle countless trivial matters—
Night patrols, facility repairs, routine safety inspections, punishing students caught breaking school rules, checking lists when upper-year students went to Hogsmeade Village...
Of course, the caretaker also handled other miscellaneous tasks, such as cleaning.
The House-Elves of Hogwarts cleaned the entire school, but they would not voluntarily appear before students. So if a large mess appeared in a public area during the day, the caretaker had to clean it up.
And every other matter that technically fell under no one's responsibility but had nevertheless happened would ultimately land on the caretaker's head.
Overall, it was a castle steward with little authority but an incredibly broad range of duties.
The workload was extremely burdensome for a Squib. Everyone else at the school had magic, so few people probably realized how long it took a Squib to accomplish something they could do with a wave of their wand.
There was another key point: the caretaker's core duty was to uphold and enforce school rules. How was a Squib... supposed to catch students breaking those rules?
Even if they did not dare cast spells directly at the caretaker and risk thoroughly offending the Hogwarts professors, escaping from a Squib was far easier than escaping from