Hey,

• in a follow up to an earlier answer I talk about this question; and in some more length in that thread about judicial and political effects of European contact in central Mexico.

• and in another thread I discuss Spanish control over colonial Mexico and resistance to it.

In order to not just throw in these older (quite long) answers here I'm summing up their main points below, hope this helps:

The Aztec Triple Alliance was dominated by the Mexica (of Tenochtitlan) decades before the Spanish conquest. While different native groups had different reasons to join forces with the Spanish, resistance to the Mexica was a common thread : For tributary states, the tributes they had to pay to Tenochtitlan were seen as too high ; for enemies of the Triple Alliance like Tlaxcala, resistance also made sense, as a way to escape the isolation their state was in, surrounded by Triple Alliance territories.

And even former members of the Alliance switched sides : the Acolhua were in the grips of a civil war at the time of conquest, with the faction opposed to the Mexica providing assistance to the Spanish. The point being that there were a variety of reasons for siding with the Spanish, but that for many Nahua groups it made sense in order to overthrow the Mexica who were often perceived as « tyrannic ».

How the Tlaxcalans and others perceived themselves during the conquest is hard to answer – our only eyewitness accounts come from Spaniards (who don't mention native allies all that much). Native accounts come starting in the mid-16th century, and are already colored by the colonial society. But briefly put, these native histories highlight both the centrality of the large numbers of native allies to the conquest (which was for real), and the special importance of their own state to the conquests' « success » (which is more debatable in each case).

I'd argue here that the native allies' position was somewhere in between those two poles : clearly the Spanish could not have managed to overthrow the Mexica without the massive help of Tlaxcalans, Huejotzincans and others, which they would have probably been aware of. On the other hand, the Spanish did have some serious military advantages vis-a-vis their allies (e.g. swords and horses) due to which e.g. the Tlaxcalans would have probably seen themselves as the most important native allies but under Spanish command.

The Spanish initially left many native rulers in power, as subordinates to the Spanish Crown; and made possible lawsuits by indigenous elites and even commoners to litigate for their rights before courts. In addition, both conquistadors and native nobles at first profited from intermarrying to forge dynastic connections and legitimacy. These together with various other factors - a major one being the increasingly devastating epidemies - meant that there was serious incentive for many Nahua states to accept the Spanish as one more among a longer lineage of conquerors in central Mesoamerica. This did not mean however that Spanish rule was secure in the early colonial period.

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I'm discussing the question of when the Spanish rule was pretty much secure over colonial Mexico in more detail in the 2nd answer I linked to, so just the main points here from that one: the Mixton War in the 1540s was probably the last serious challenge to Spanish overrule in colonial Mexico. This was a major military campaign by the Mixtecs that was only won through the Spanish through personal intervention by the viceroy.

Looking further afield though, the Spanish never controlled all of New Spain (the name of the Spanish viceroyalty then) – as was the case in many other parts of Spanish America. Two areas that would prove esp. difficult to conquer and raised resistance throughout colonial times were Northern regions (like Nueva Galicia and Nuevo Mexico), and Yucatán.

These led to major Spanish campaigns with important assistance of native allies throughout the 17th c. and later, not always successful. So that while central Mexico was an important imperial centre by the mid 16th century, other regions of central America were only partly or not under full Spanish control throughout the colony.