From the point of view as a primarily jazz player that later in my career spent a lot of time in an orchestra I think the hypothesis is an oversimplification, and probably due to the eg. pop musicians who state it misunderstanding the skillset needed for a 'classical' musician.
I have experienced rehearsing an orchestra playing a piece by Franciax, a 20th century orchestral composer who used a lot of other 20th century styles in his composition. The rhythm in the strings was to be played as a clave, a relatively exotic rhythm in the most vanilla sense, and the orchestra fell apart regularly for the first few sessions. This is in a fairly good quality but definitely amateur orchestra.
In the same orchestra, another piece, I was sweating and barely keeping up with bars of odd numbers and dramatically changing tempo while the rest of the orchestra just followed the conductor and happily played it like they were taking a walk in the park.
Now you could not say the orchestra had bad rhythm, they could easily play the second piece, while I could easily play the first piece, without thinking, respectively. I have many other examples of playing rhythms in orchestral pieces so odd to me as a 'pop' musician that I couldn't get my head around them. I'd show my jazz friends what I was playing and they would all chuckle at how odd it read. Yet the music created was highly rhythmic, and arguably couldn't have been conceptualised in any better way than how it was written.
I think the stereotype comes from the huge difference in approach. An orchestra has a conductor dictating, often manipulating, the time heavily. The orchestral musicians role is to place their notes, sometimes with odd rhythms, exactly in keeping with the conductor, though often compensating for the whole orchestra being a bit behind or the sections they are meant to align with playing freely etc. It's a very organic, very musical, approach to what 'rhythm' means where any one player could ruin the whole sound and getting a good sound is only possible if everyones senses are at 100%, playing their part in the highly complex 'event' they are involved in.
On the other hand, pop/jazz musicians are very used to being given a starting tempo and then sticking to it ABSOLUTELY. Dragging a bit being a cardinal sin that may get you fired from a session. A 'groove' is set up and then we all feed into that grove with our playing. The millisecond differences that make a pop/jazz musician groove or sound flat are just as nuanced as the millisecond differences that make an orchestra sound very together, or messy. And again, one player being slightly off can completely destroy the groove of the whole ensemble.
It's easy for a pop/jazz musician to, to use my first example, play a clave over a fixed tempo because we are used to taking a rhythmic phrase over a set pulse and placing everything accurately bar after bar for many measures of unfaltering tempo. Most such musicians learn many complex rhythms over a fixed tempo and learn how they feel when repeating over and over and refine, refine and refine again till it sounds better and better, pushing and pulling beats to create a particular groove, including all sorts of idiomatic conventions of 'how to make it lazy' or 'how to make it pushy' to give the music a particular feel.
When you eg. hire a classical player to play over a pop record they may not have this library/muscle memory of repetitive bars with an exact groove feel for each one, they may play looser or tighter, or not respond to eg. where the drummer is framing the rhythm in a particular way.
But again, place a funk musician in an orchestra playing eg. La Mer, and they would be LOST, it's EXTREMELY hard, I say this from experience.
So the trope of orchestral musicians having bad rhythm is very wrong, they have exceptional rhythm. But the set of circumstances playing in an orchestra compared to a funk jam is very different, and due to popular music being the widespread 'sound' they get unfairly labelled as having 'bad rhythm'.
Of course, good musicians of either area of music will quickly adapt and hear what's needed of them, some of the most impressive classical musicians I have heard can storm a jazz jam then wander off into the sunset while the houseband are still recovering. Much less often do I hear of a jazz musician mastering an orchestral situation with the same authority, in fact I'd say the first rehearsal for them is almost always a huge eye-opener.
So, maybe the question should be 'why are orchestral musicians so able to deal with very complex rhythms over a constantly changing tempo when jazz/pop musicians can't?'. I'm being a little inflammatory of course ;) The rhythmic skills of the pop/jazz musician could take a lifetime or more to master, but the same goes for the orchestral player. The simple answer is that they are very different skillsets.