Clientside Java pissed off developers: unstable plugin, no backwards compatibility whatsoever.
Clientside Java pissed off average Joe: unstable plugin, guaranteed browser freezes, constant nagging for updates shipped with nasty toolbars.
Clientside Java pissed everybody off. So there. That's the problem right there. You can't blame aforementioned Joe for a healthy aversion regarding Java, trying to obliterate every single JRE he can find, for the sake of browser security, too.
No! The Java applet plugin pissed everyone off. Every copy of Matlab embeds a JDK, just like Wakfu, or the Windows version of IntelliJ (IIRC). That is all client side and there are no complaints about that at all.