Yes and no.
Duo's correct translation for "Money is the root of all evil" is "Geld is de wortel van alle kwaad." However, that sounds unnatural to a native Dutch speaker. The correct idiomatic translation is "Geld is de duivel van alle kwaad." Duivel means devil.
As for your example, "That is the root of the problem," while you could use "wortel" there are other, more acceptable, ways to phrase the sentence. For example, "Dat is het begin (the beginning) van de probleem" or "Dat is de kern (the core) van de probleem.
These may differ from Duo's accepted answers, but keep in mind the course is currently still in Beta.