I’m no lore expert but I assume it comes down to a consideration of relative numbers & size, priorities & interests.
Numbers: Capsuleers are supposedly an elite. For every one of them there are millions of normal citizens who are born, live and die within Empire controlled space. This means that even if pod pilots are ignored, the Empires are the most densely populated area of New Eden and those people are the single most valuable resource available.
Size: These Empires have grown and progressed as a result of the labour of their numerous citizens and their combined strength is considerable, as evidenced by the efficacy and pervasiveness of CONCORD. Their individual pilots may lack the resources available to pod pilots but they have the advantage of numbers, using them to police their space every minute of every hour of every day in a way that even the largest capsuleer Empires can only dream of.
Priorities: Capsuleers are focused on building their own empires in unclaimed/disputed space but they need the resources of the four racial Empires to achieve this. They obtain new recruits from Empire space and acquire a great deal of manufactured goods, while selling their own produce at Empire market hubs. Put simply, Empire Space is good business, for citizens and capsuleers alike, so why attack and destroy something that keeps you in ships and modules and can even make you rich?
Interests: Unlike the four racial Empires, capsuleers are a divided lot, with different vested interests and changeable loyalties, hence they’re unlikely to ever unite for long enough and in sufficient force to take on and defeat even one of the racial Empires, much less all four. Instead, they’d rather fight each other over control of the richer but less easily defended nullsec space which none of the Empires lay claim to.