Eritrean nationalism was more complex than what your perception appears to be of it. The traditional area of Ethiopia is an incredibly diverse region, and during the period of the Derg regime and concurrent civil war, ethnic-based rebel groups popped up all over the country. There were Oromos fighting in the south, Somalis in the East, and Tigrayans in the north. The Eritreans were largely Tigrayans as well, and not too surprisingly there would be a lot of cooperation between the Ethiopian Tigray People's Liberation Front (TPLF) and Eritrean People's Liberation Front (EPLF).

The ethnic strife was an issue that stretched back to the regime of Haile Selassie. Selassie was of the Amharic ethnic group, and part of his postwar efforts to consolidate his rule and modernize the country involved suppression of non-Amharic culture. Eritrea's Muslim minority was among the more prominent victims of Selassie's cultural efforts, which left Eritrea's (and Ethiopia's) Muslim largely disenfranchised. Even non-Amharic Christians suffered, however due to the priority given to the Amharic language and writing. Amharic Ethiopians make up less than 30% of the country's population, and such policies left the majority of Ethiopia's ethnically and linguistically diverse population largely disenfranchised.

Eritrea's rebels stood out, however, because of their colonial legacy. In a pattern you'll find in a few areas across Africa, the decades of colonial administration tend to create some sense of national identity, if due to nothing else than the population becoming accustomed to a certain style of administration. A similar prominent case is the separatist movement in English-speaking western Cameroon, which stems largely from the largely English-speaking formerly British-administered western region feeling alienated and poorly represented by the remainder of the country, which was a French colony and thus speaks French. Eritrea experienced something like this. Italian administration, while foreign, helped nurture a separate identity. After WW2, a movement within Eritrea hoped for independence, with a variety of plans floated. Unfortunately for the independence movement, the UN made the decision to award the region to Ethiopia in hopes of mitigating independence-minded sentiments with a more "local" administration and accounting for Ethiopia's claim on the region. Part of this deal, however, involved the establishment of a separate democratic administration, which Ethiopia, at least for the time being, would oblige to.

As the 1950s went on, the Selassie regime grew incompetent due to the ruler's age and refusal to delegate power. The poorly thought out cultural practices alienated many ethnic groups, but in a population that had a recent history of separateness from Ethiopia as well as a separate, nominally democratic administration, it helped to further solidify secessionist sentiment. When Selassie revoked Eritrea's special status in 1960, it only served to widen the gulf between the two. Selassie's regime would do a fairly good job keeping the movement suppressed until its fall, but when the Ethiopian revolution happened and the Derg regime took over, the Eritreans were able to take advantage of the weakened state of the country to launch their armed struggle again. As the civil war continued, the Derg regime would make many of the same mistakes as Selassie, only further cementing the idea that Eritrea must become independent.