"It's doubtful she will come."
The subjunctive is used to indicate some feeling towards a subject or uncertainty.
In the first sentence, the verb "know" is used. If someone "knows" something then it is right to them, and the subjunctive is not used.
In the second/third sentences, the adjectives true and certain are used. (Both of which are apparently synonyms to each other.) Since that there is certainty in these two examples, the subjunctive isn't used once again.