I think there were so many things.

Apple already had an ecosystem from the Classic Mac OS. It had lots of apps, lots of loyal users, etc. It had issues, but Apple wasn't starting from scratch.

BeOS was simply new. That means trying to get everyone to support a new platform. If you weren't a Mac user back in the day, you might not know how hard it was - getting printers to work, having to buy Mac-specific accessories, etc. The Mac would have millions of users while BeOS would have none. Getting third-parties to support the platform would be incredibly difficult - it was so hard on the Mac already. This was way before a lot of work on platform independence. Also, if you'd run Linux 15-20 years ago on a laptop, you probably remember the issues around stuff like getting WiFi to work. BeOS was trying to launch a new ecosystem in an era before the web really took over and when native apps and drivers were important and not cross-platform.

Maybe think about a different question: why did Windows Phone fail when the iPhone and Android didn't? Well, it was a third platform and an also-ran with almost no marketshare. Developers didn't want to support a third platform when users saw no need for it. Users didn't want to buy into a third platform without apps.

Still, one of the major things for Be was that Microsoft forbid OEMs from offering BeOS on their machines - if they wanted to be able to get Windows OEM licenses. So Be was locked out of every PC company. If you were Dell, you might tell Be, "we'd love to offer customers the option of getting a Dell with BeOS, but we can't because we need Microsoft's Windows licenses." So if you bought a PC, it'd come with Windows and then you'd need to buy BeOS and install that. Now you had a great OS with nothing to run on it and you'd go back to Windows. Be did make BeOS free at one point, but it was too late (and even at free it lacked a reason to be run).

The Mac had built up marketshare, a userbase, application support, drivers, etc. for a decade when BeOS launched. BeOS launched at a time when Microsoft had sewn up the PC market and was in its full-monopoly, anti-competition stance. They used their power to crush all rivals on the PC.

Apple, even though they had some limited clones, was never really a rival. Apple was a hardware/software combo play and small enough to be ignored as a declining niche player. Did Microsoft "save" Apple? Probably not. They did invest some money and committed to make Microsoft Office available on Mac which certainly helped (remember, this is before the age when things could read .doc and .xls files and Microsoft was still in anti-competition mode where they'd try and break competitors products).

Still, it seems more like Microsoft wanted to keep one player around to stave off anti-trust concerns - and Apple was the safe one to keep around. If they kept Be around, BeOS would need to get some meaningful marketshare (let's say 5%). At that point, what's to stop more people from running BeOS? Nothing - their Pc could just run BeOS. If they kept Apple around with 5% marketshare, what's to stop more people from running MacOS? The fact that they'd need to buy new hardware from Apple at a premium price point with inferior capabilities. That's safe. People can't switch. And Intel was killing PowerPC processors at the time and PCs were available for $500 while Apple finally introduced a budget machine at $1,300. Here's a $500 eMachines with 300MHz processor or an iMac for $1,300 and 233MHz processor - and things got worse from there as the years went on. The point being, Apple was never a threat to Windows because MacOS was tied to separate hardware. BeOS was a huge threat to Windows if Be got any traction. They needed to be killed.

Apple's real resurgence wasn't via Mac OS or even Mac OS X. It was via the iPod. They just started making so much money. Money means you can invest in things. Then the iPhone meant even more money. Then their computers were still expensive, but had a much lower premium than they used to - especially if you account for things like display quality.

Maybe Be could have launched a BePod, but they didn't. Maybe Be could have parlayed that success into a BePhone. Maybe Be could have used all that to become a player on the desktop. But they built the BeIA internet appliance which was just a computer, but worse. Apple removed the floppy drive and Be removed both the floppy and CD drive - at a time when computers were becoming music hubs.

BeOS launched in October 1995. Apple bought NeXT in 1996 and launched the iMac in 1998 and iPod in 2001. BeOS was such a flash in the pan. Blink and you'd miss its 5 year existence. BeOS R5 (the final released version) came out in March 2000, less than 5 years after the initial launch. In a lot of ways, they never really got any traction - but they did get a lot of love from the people who used it. BeOS was magical in many ways (even if somewhat unfinished in others). At a time when the Mac OS had cooperative multitasking and would just freeze up, at a time when Mac OS X was unusably slow, at a time when Windows was a jumble of crap that never quite worked right, BeOS was this clean, modern, happy system. In many ways, it had Mac-like polish and coordination to it combined with such a modern developer experience and so many great ideas.

But it's hard to get over the hump necessary to create the momentum that brings developers and users. Apple already had those users and developers (even if it was a small community compared to Windows). Then Apple had some amazing hits with the iPod and iPhone.