The Spanish conquistadors were small in number and thus used divide and conquer tactics to gain indigenous allies to even the playing field numerically during their conquest of the Americas. Even though they assisted the Spanish, they would eventually turn on them. Do we have any record of any former indigenous allies to the Spanish realizing they made a mistake or regretting supporting the Spanish? Once the indigenous allies realized the Spaniards couldn't be trusted, why weren't there widespread revolts to push them out? With their small numbers and no indigenous allies this time, shouldn't it be relatively easy to defeat the Conquistadors?
You're absolutely right that the Spanish campaigns would have been impossible without their indigenous allies, who mostly outnumbered the Spanish massively - often these were more wars between different native groups than Spanish "conquest" wars.
For the rest I'd have to answer with a few important caveats, and add longer answers in the end:
An issue for knowing direct reactions by native allies is that we simply don't have indigenous eyewitness accounts from that time, in contrast with the Spanish conquistadors' accounts. So eg in central Mexico no Aztec pre-Hispanic sources have survived. Instead we do get writings by especially Aztec and Inca authors- but also from other groups - decades after the conquest campaigns. One main reason being that it took some time to actually learn alphabetic writing as well as European languages.
More importantly, at least in central Mexico until ca the late 16th century it was not at all clear that native elites were worse off than before - excluding of course the massive demographic catastrophe. Since in both that region and in Peru that Spanish built on the Aztec and Inca socio-political structures, the elites could often retain power, at least until the Spanish no longer needed their influence and power. So for many groups, again in central Mexico, there was certainly the expectation of getting rid of the Mexica's ruler's and excessive tributes - which at first did work out, although more for some groups than for others.
Lastly, there actually was major and continuing resistance to Spanish rule in many regions of the Americas, throughout colonial times. Violent rebellions took place on large scales especially in the Andes, Yucatan or in (modern-day) northern Mexico. So that strong Spanish control was generally strongest in the centres around Mexico City and Lima, but heavily decreased the further you got. Additionally there was less obvious forms of resistance like urban uprisings that did not challenge Spanish rule, but showed it's fragile nature.
I go into more detail on this for Mesoamerica, especially in these answers (heads up they're long!):
in a follow up to an earlier answer I talk about your 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.
Hope this helps!
The Tlaxcalans, the largest indigenous group to side with Cortes, did rather well out of the exchange, as /u/jolex41 answer here explains. It isn't actually clear they did make a horrible mistake, at least from the perspective of their rulers, unless one imposes an ahistorical pan-indigenous perspective on them.