Learn Spanish (Latin America): Si cuestionas el sistema, hay consecuencias. - If you question the system, there are consequences.

Preguntar means to ask a question to get information. Cuestionar means to challenge, dispute, or express doubt about something, which fits the context of challenging an authority or system.

Since questioning the system is a hypothetical situation, why don't we use the subjunctive here?

In Spanish, you never use the present subjunctive immediately after si (if). Because this is expressing a general truth or a likely conditional outcome (if A happens, B happens), we use the present indicative. Saying si cuestiones would be grammatically incorrect.

Why is it el sistema when the word ends in an 'a'?

Words ending in -ma that are originally from Greek are almost always masculine in Spanish. You have likely seen this rule in action with other common words like el problema, el tema, and el idioma.

How would I use the discourse markers from this lesson, like al fin y al cabo, with this sentence?

You can use them to emphasize the inevitable result of the action. You would typically place the marker right before the consequence: Si cuestionas el sistema, al fin y al cabo hay consecuencias. (If you question the system, at the end of the day there are consequences).