I always loved Warcraft and Starcraft's single player campaigns. Those stories were epic as anything made today, especially for 1990's pre-teen me. Dark as hell, yet surprisingly family friendly. Bunch of years later and I found Halo Wars was pretty similar, but on console.
My read on things is essentially this:
1) Blizzard post-Activision acquisition got out of the RTS genre almost entirely; they were a steam engine for that genre that could have almost single-handedly kept demand for it up via Warcraft and Starcraft
1b) World of Warcraft's influence on the above point cannot possibly be understated. It was far cheaper and easier for Blizzard to carry the story forward in the MMO medium once the framework was established rather than pumping out a new game with new graphics and entirely new assets every few years. Even without Activision, Blizzard ultimately would have let the Warcraft RTS games wither at the vine once WoW became a hit that just kept hitting for a solid decade plus. Furthermore, WoW nabbed more players than the first three Warcraft games ever did, and combined with monthly subscription fees, made Blizzard a hell of a lot more money too. The only reason that Starcraft 2 and Overwatch got made at all was because Blizzard was smart enough to realize that the free-flowing tap of money had started to slow into a comparative trickle.
2) Ensemble studios died before Halo Wars even actually released, which took the other king of the RTS field out of commission. I honestly feel lucky that we got a finished product at all, but events are what they are and Halo Wars wasn't going to have been the savior that reversed Ensemble's financial hemorrhaging.
3) the RTS genre was simply never actually that big to begin with. The loss of its two biggest players inside of just a few years pretty much tanked the whole thing. It's hard to make money selling these sorts of games too as they lack the broader appeal of MMO's or Shooters. Ensemble, for its part, had been hurting for years as they routinely failed to sell as much of their new games as the game before had sold, and game development is itself an expensive proposition. It gets even harder when you're trying to develop a new game and you only just broke even on your last Hero Release.
Which brings me to the ultimate reason:
The Market moved on. RTS was always something of a niche market because while its fans have been and will always be dedicated to the ends of the Earth, its a proven fact that its very difficult to convince new people to buy into becoming fans. Advertising is a big factor: bigger and bolder RPGs, Shooters, Racing Games, MMO's, Fighting games, and even puzzle games like Portal are historically of broader appeal and easier to advertise and sell. Starcraft is unlikely to ever move as many copies as FIFA or Call of Duty in the same year. Once it became clear that the RTS target audience was not growing, and merely staying the same, developers moved on to something with more market appeal.
Now there's a silver lining on the horizon: Clash of Clans.
CoC and all of its ilk, while not true RTS games, have begun to pave the way for a resurgence of strategy based games on mobile devices, a field that DOES make a lot of money for relatively little development cost. RTS games could easily find a new home on phones and tablets, with the larger screen sizes current mobile users preferring already being in favor of the sprawling information-dense user interfaces that typically accompany an RTS.
RTS games will never be the must-have-hit of a given year of gaming, but after a lengthy sleep, it's entirely possible they may find new success on mobile.
We can only hope.