If 'le Fait Que' Is Supposition, Use the Subjunctive

The subjunctive after le fait que (the fact that) is optional: It depends on what you mean.
When you're actually talking about a fact, you do not need the subjunctive, as in:

Le fait qu'il le fait
The fact that he's doing it
(You know for a fact that he's doing it.)
However, when you're talking about a supposition, you do need the subjunctive, as in:
Le fait que tout le monde sache
The fact that everyone knows
(You're supposing that everyone knows, but you don't know it for a fact.)

The Heart of the Subjunctive

This goes to the heart of the subjunctive mood, which is used to express actions or ideas that are subjective or otherwise uncertain, such as will/wanting, emotion, doubt, possibility, necessity and judgment.

The subjunctive can seem overwhelming, but the thing to remember is: the subjunctive = subjectivity or unreality. Use this mood enough and it will become second nature...and quite expressive.

The French subjunctive is nearly always found in dependent clauses introduced by que or qui, and the subjects of the dependent and main clauses are usually different. For example:

Je veux que tu le fasses. I want you to do it.
Il faut que nous partions. It is necessary that we leave.

Dependent Clauses Take the Subjunctive When They:

Contain verbs and expressions that express someone's will, an order, a need, a piece of advice or a desire.
Contain verbs and expressions of emotion or feeling, such as fear, happiness, anger, regret, surprise, or any other sentiments.
Contain verbs and expressions of doubt, possibility, supposition and opinion.
Contain verbs and expressions, such as croire que (to believe that), dire que (to say that), espérer que (to hope that), être certain que (to be certain that), il paraît que (it appears that), penser que (to think that), savoir que (to know that), trouver que (to find/think that) and vouloir dire que (to mean that), which only require the subjunctive when the clause is negative or interrogatory. They do not take the subjunctive when they are used in the affirmative, because they express facts that are considered certain—at least in the speaker's mind.
Contain French conjunctive phrases (locutions conjonctives), groups of two or more words that have the same function as a conjunction and imply supposition.

Contain the negative pronouns ne ... personne or ne ... rien, or the indefinite pronouns quelqu'un or quelque chose.
Follow main clauses containing superlatives. Note that in such cases, the subjunctive is optional, depending on how concrete the speaker feels about what is being said.

Why 'le Fait Que' Sometimes Takes the Subjunctive

Le fait que (the fact that) is an example of number 4: an expression of doubt, possibility, supposition and opinion. There are many expressions in this category and for all of them, it's the same. If they are expressions of uncertainty and subjectivity, they, of course, do take the subjunctive. When they talk about an actual fact, they do not take the subjunctive. So think before you write or speak these common expressions, which most times take the subjunctive: