Here's why:
* Certain means having no doubt; sure.
* Questionable means doubtful; uncertain; suspicious.
While they are related in that they both deal with a lack of certainty, they are not direct opposites.
Here are some actual antonyms for certain:
* Doubtful
* Uncertain
* Unsure
* Possible
* Probable
* Unlikely
Think of it this way:
* Certain: I am certain that the sun will rise tomorrow. (There is no doubt)
* Questionable: The evidence presented is questionable. (It is doubtful or suspicious)