What is Cather saying in these two quotes, and what is the larger meaning?
"On the farm the weather was the great fact, and the men's affiars went on underneath it ..."
"Look at my papa here; he's been dead all these years, and yet his is more real to me than almost anybody else ..."
The rest of the passages surrounding these quotes serves to give them some context and provide a better explanation.
For example, regarding the weather, it is suggested that this is similar to how "streams creep under the ice". There is motion, but it takes place under a great, immovable object that dominates the action. The weather is the "great fact"; while our lives change, and we worry or make plans, there above us is the weather, literally hovering over us and confronting us with plain reality that we cannot ignore.
The larger meaning of this passage is a reinforcement of the imagery of the American West that Cather works so hard to convey; nature, to the pioneers, was a huge and powerful thing that made human efforts seem small and ant-like by comparison. This serves both to champion the spirit of the people toiling under these conditions and to paint the wilderness as an entity itself.
The passage about Antonia's dead father also explains itself; she concludes "The older I grow, the better I know him and the more I understand him." Her father, despite being dead, has never been gone; his presence in her life continued after his death in form of memories and lessons that, perhaps, she was too young to fully comprehend at the time, or that contemplation has added depth to them.
The broader meaning is that people who are important to us make a lifelong impact on our lives, and that physical separation does not influence that heritage. We may even draw an analogy to the position of these characters as orphans and immigrants, that they are never truly alone, but continue to draw strength from their origins. Jim, commenting on Antonia's memory, mentions "immemorial human attitudes which we recognize by instinct as universal and true" - in some sense these are not just memories, but essences, which compose part of the human experience.