The opposition had an interest in returning to conservative policies
Morales was born to an Aymara farming family and grew up in the department of Cochabamba, home to the main producers of cocoa leaves in the country. Growing up he distinguished himself as a union leader who defended the rights of cocoa farmers and presented a socialist platform with strong advocacy for indigenous communities (which represent more than 60% of Bolivia’s population).  The presidential candidate Bolivia’s opposition fielded in the October election, Carlos Mesa, is a “pro-business” privatizer with extensive ties to Washington. US government cables published by WikiLeaks reveal that he regularly corresponded with American officials in their efforts to destabilize Morales.
Morales was Bolivia’s first indigenous president and the only one who had ever served the interests of its indigenous population, bringing down extreme poverty rates from 38.2% to 21.65 in only seven years, increasing literacy and reducing chronic undernourishment.  The opposition leader, Luis Fernando Camacho, is a paramilitary Christian fascist, who vowed to defend Bolivia holding a Bible in one hand and a national flag in the other. He has supported Bolivia’s new president, Jeanine Añez, and has received the support of right-wing leaders across the continent, such as Brazil’s Jair Bolsonaro. The de facto government has already defaced indigenous symbols and insisted on the supremacy of Christianity over indigenous traditions, leading to a surge in racism and outrage among indigenous protesters who demand respect for their culture and traditions. 
Morales ability to increase social spending has been directly linked to the increased value of Bolivia's natural resources, and not necessarily to Morales indigenous background. For many indigenous groups, this economic bonanza has come at an extremely high cost. Morales has led the careless extraction of natural gas, along with an increase in mining activities, at the expense of Bolivia's rich natural environment. Indigenous groups have also stood against Morales over his disregard for expanding indigenous land rights.  Moreover, it is not a requirement for a leader to be indigenous in order to care about a country's indigenous population.
The opposition had a racist and classist intent to overturn the government and return to policies that would favor the rich elite of European descent. Accessing power in the aftermath of Morales' resignation, they capitalized on this unrest and took a swift turn towards anti-indigenous policies. This shows there was always an intent to take control of the government to benefit the rich elites.
Rejecting the premises
Morales only favored indigenous groups because he had the economic capacity to do so, and it benefited him politically. Morales did not look after small indigenous communities that occupied the land he needed for natural resource extraction. Morales did not care about indigenous groups beyond his own needs.