Translation:What is ordinary is not special.
This isn't necessarily disagreeing with what has been said here, but I think there is something to be added to this discussion.
To me, the word "ordinary" describes something with lack of apparent special features, or something that is very common. The word "special" describes something either being precious or distinctive.
So, I would say that ordinary things are often special. To consider things like basic liberties and freedoms, loyalty to friends and family as ordinary (after all, they are quite common, at least in the places where I have lived) and therefore of lesser value is a big mistake. These things are often the most important; they have become common because of their value, not in spite of it.
"I was raised up believing I was somehow unique,
Like a snowflake distinct among snowflakes, unique in each way you can see.
And now after some thinking, I'd say I'd rather be
A functioning cog in some great machinery serving something beyond me."
~Fleet Foxes, Helplessness Blues
Yes, it's fine.
"What is ordinary" is a headless relative clause -- you could consider it an abbreviation of something like "Something that is ordinary".
The clause "What is ordinary", as a whole, then can be used grammatically much like the "something" could be used - for example, as the subject of "___ is not special".
If you omitted the commas, I would agree with you, but with the commas - where "which is ordinary" is a non-restrictive relative clause - I think it doesn't work as a translation of this sentence, because then the subject is missing.
Your sentence could be a translation of "Tio, kio estas ordinara, ne estas speciala" (I would put the commas in Esperanto as well).