My guess is that custom proteins are harder to synthesize on demand. Generally if you want a custom protein you synthesize the DNA coding it, then insert it into a cell and have it produce the protein. Plus, DNA can be duplicated in vitro through conventional PCR where it's not really viable to transcribe proteins outside of a living cell.
While this is certainly all true, it is not the main reason. The main reason is design complexity. Single stranded DNA (ssDNA) has a really easy set of association rules; A pairs with T and G pairs with C. DNA origami is constructed of a viral DNA and many many DNA "staple" oligos, so the folding of DNA origami is actually done by one big dna molecule annealing to many shorter ones, which coax it to fold into cool shapes.
If you compare this to proteins, which are strings of amino acids, which don't have
Source: http://rss.slashdot.org/~r/Slashdot/slashdotScience/~3/cveAbB2CXws/story01.htm
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