Sure it would be nice if margins were larger, however at the end...

Sure it would be nice if margins were larger, however at the end of the day Market Cap will be a reflection of NPAT. If they can squeeze $3M NPAT from $100M revenue, I'd be okay with that. Using the $3m work out how much capital would you need in bonds yielding 5% to make $3M? ($60M!) That gives you a ballpark idea of what this company could be worth in the longer term. Of course, running a low margin business is risky, so you need to discount the value accordingly; however, it's still maybe double the current market cap.
Also if revenue keeps building the market cap will increase accordingly and also the goodwill becomes a factor as its worth more to a bigger fish wanting to grow or just wanting to take a competitor.
So I'm pleased to own this business right now even with the low margins.