(The pasuk from Malachi is read as the haftarah of parshas Toldos.)
I think we need to just read the next few pesukim to understand this inyan. The Novi is saying, that Hashem loves us as a nation, but we have turned away from Him. “If I am your Father, where is My respect; if I am your Master, where is My fear?”.
Maybe the pshat is, that Hashem loves us despite the fact that we have turned away. Like a father whose child has strayed, He constantly waits for us to return.