I think Microsoft did take them seriously. They just screwed up the execution.

Like here's a "Microsoft’s Windows Mobile 2003 for Pocket PC Phone Edition" phone out a couple of years before the iPhone https://www.zdnet.com/product/anextek-sp230/

As I recall, the iPhone originally had little to none integration with enterprise infrastructure, as Blackberry and Windows Phone had . In my view, The iphone was just too cool not to be in the hands of CEOs and CTOs , which most likely managed to bend companies rules to start allowing usage of iphones and basically making blackberry superfluous

Their problem with execution was the plan of vertical integration that Apple is known for. In particular, there's little that the first iPhone could do that Blackberry didn't already do at the time - except for one thing. Cost. Blackberry was a victim of their success in the business market segment, and Microsoft wanted to join them there. The iPhones initial launch included a deal with AT&T to make it a relatively affordable, consumer facing device, thus expanding the market as a whole, to the success we see today.

Perhaps they thought they could deal with it in their own time. Instead, the world marched on.