According to Tosfos DH 've'Yesh Omrim', there are two kinds of Am ha'Aretz. Both are ignorant in Torah learning, only one knows that he ought to learn and has deliberately gone astray; the other (who is generally referred to as 'Tinok she'Nishba') is blissfully unaware of the value of Torah-learning.

The latter may well be unaware, and therefore will not be severely punished for his failure to study Torah diligently, because he is a Shogeg or an O'neis. This does not alter his status however, and explains the six things that the Beraisa says about him; because at the end of the day, without Torah, a Jew cannot know how to conduct himself, and is therefore bound to make many major mistakes, even in his dealings with others. Presumably, this is also the Am ha'Aretz about whom the opening Sugya (concerning marriage) is referring to, since the constant clash of interests between a Talmid-Chacham and a bas Am-ha'Aretz who are living together, is bound to have severe ramifications and bitter consequences.

R. Elazar on the other hand (who forbids accompanying an Am ha'Aretz on a journey, and who allows killing him on Shabbos Yom Kipur), is speaking about an Am ha'Aretz who knows that Torah is synonymous with life, yet he rejects it (as the Gemara says 'If he doesn't "value" his own life, there is no reason to assume that he will "value" yours').

I assume that this is the section of Gemara that you find difficult, and like you intimated, the Amei ha'Aretz of those times hated the Torah-Jew with a vengeance. It is possible that these Amei ha'Aretz fall into the category of Minim, too.

I not sure that R. Elazar is exaggerating, as human lives are at stake here. The commentaries too, seem to take him very literally, although the poskim explain that his rulings do not apply nowadays.

Be'Virchas Kol Tuv

Eliezer Chrysler.