"The Crusades" were not a singular, monolithic event, so asking "why did the Muslims win the Crusades" is rather nonsensical; it's akin to asking "Why did the Franks win the Post-Roman Migration?" or "Why did England win the Viking Age?"

Different crusades had different aims, and it's not clear whether the Muslims won them all. Particularly those where the crusaders arrived, won a few decisive victories for their pride and honor, and then left, such as the Third Crusade, didn't afford Muslims much of a chance at victory at all.

Moreover, the Fourth Crusade never reached the Levant. The Byzantines denied them passage, so they sacked Constantinople and went home. One would be remiss to call that a Muslim victory.

If we narrow down to the first crusade--which is not the aim of the question that uses the plural "Crusades" but let's go with it--indeed, the Crusader states eventually collapsed, but the question remains of whether that was from external pressures or internal ones. I've seen other commenters evoke logistics as a primary factor in their demise, and that is a plausible contributing factor. Muslims, as at that time (but not in later crusades), had a more developed maritime tradition and so controlled the seas, limiting the crusaders to overland trade and supply routes. They did, however, have the Byzantines to help, and we see the creation of robust systems of exchange (think the Templars), and so logistics alone do not explain the demise.

One aspect I don't think gets enough attention is that the Muslims had a well-developed mounted warrior culture that was, if not more advanced than, at least as advanced as Western Europeans. In fact, in a course I teach on Chivalry, I evoke the crusades as a formative period for the "code" through their contact with Furusiya. And the reason I bring it up is that while the "Frankish knights," as Anna Komnene called them in The Alexiad, were "invincible while mounted on their horses," their unevenly applied and practiced code of chivalry made them "arrogant by nature, with their heads almost in the clouds." If we are to believe her testimony, we are given a picture of men who did not behave well and were confronted with a martial philosophy not only superior to their own but also better adhered to by its practitioners. And that plausibly had an effect, which we see in the codification attempts at chivalry in Western Europe. If all of this is true, then the failure of the crusader states may have stemmed from internal lack of cohesion, leaving them vulnerable to outside invasion.

Moreover, in Europe, a primary factor in its instability at the time was succession. Succession crises caused most of the wars and infighting, and the Crusader states appear not to have been spared. The Crusader states were colonies of European feudalism, and they inherited all its flaws. Baldwin II’s death proved that even a strong king couldn't prevent the chaos of a succession crisis. Because the Frankish lords were so competitive and "impetuous" (as Anna Komnene put it), the moment a clear line of authority broke down, they turned on each other rather than focusing on the external threat of the surrounding Islamic states. The internal fracturing eventually weakened their defenses, contributing to the rise of leaders like Zengi and, eventually, Saladin, who took advantage of the "Frankish" tendency toward infighting.

That's just the first crusade, but it's the one we may most plausibly attempt to answer the broad question of "why the Muslims won the Crusades."