We always have breakfast IN the morning. We always have brunch AT noon. We always have lunch IN the afternoon. We always have dinner IN the evening. We always have an Alka Seltzer AT night. Do you see a trend?

in the morning

The preposition "in" is correct here. When you are talking about a general time (morning, evening, afternoon, daytime. nighttime, etc.), then you use "in." This is because these are all periods of time, spanning more than one specific moment. So it's "in" that time period. "At" would be used for a very specific time. For example, let's change the sentence. "We always have breakfast AT 9:00AM." Since the time is a specific moment, we use "at."