the meaning of "Non-primary hits" and "tags"
"tag" is a weird term in this context. It used to mean "read", but RSeQC likes using it in an odd way. Suppose you have a read that aligns to a single contiguous (though possibly with InDels) stretch of DNA. This would then count as one tag. Suppose instead that you have a spliced read, that is one where part aligns to one exon and part to another exon. Each aligned part of this read then counts separately as a tag. So this 1 read becomes 2 tags. By extension, if you have a read that is spliced such that is starts in exon 1, jumps to exon 2, and then finally jumps to exon 3, then it'd count as 3 tags. This is only useful if you're interested in splicing, since the higher this value is the better you're able to discern differences there.

For "non-primary hits", suppose you have a read that can align equally well to multiple places in the genome. If there are 5 equally good alignments, then 4 of these will be labeled as "secondary" and one of them will not, which is then the "primary alignment". "non-primary hits" is then an odd way of saying "secondary alignments". The number of primary alignments is equal to the number of reads that aligned.