Munich airport to Munich main train station.

The Sbahn runs frequently, and takes about 45 min. But where are you flying from? Will you need to clear Immigration first? If its an intra Schengen flight, it's on time, and you really hustle, you could do this. If you need to clear immigration - unlikely.

Thanks. We will have been in Europe 10 days prior. We’re arriving by bus from Innsbruck to Munich airport. So 45 min to get train station will work?
I just need to look for train at airport to get to Main station.Hopefully well marked

We’re arriving by bus from Innsbruck to Munich airport.

That should be enough time but you might want to check that your bus doesn't stop in Munich first before heading to the airport. Which bus service are you using? Most of them coming from the south will stop in Munich first before the airport.

DJ

We’re arriving by bus from Innsbruck to Munich airport. So 45 min to get train station will work?

As long as the bus is on time.

There are also trains from Innsbruck to Munich Hbf. No backtracking. A train is not susceptible to traffic delays, more likely to be on time. Rail ticket from Innsbruck to Munich is probably more than bus ticket, but S-Bahn from airport to Hbf is €11,60. Of course, if you haven't already bought your ticket from the Hbf, a ticket from the airport is likely the same (for a long distance) or not much more.

Also, where is your 11:30 train from Munich Hbf going? Maybe you can get it elsewhere on its route? Like Ostbahnhof or Freising.

Let's re-phrase this question:

I want to get from Innsbruck to XXX. I have a free transport on a bus from Innsbruck that is scheduled to arrive at Munich airport at 09:30 (subject to any traffic delays). There is a train from Munich Hbf to XXX at 11:30.
Is this a sensible option, or should I just take a train direct from Innsbruck to XXX?

ANSWER: You will probably make it to Munich Hbf in time, but with a bus there is always a risk of traffic delays.
If you told us where XXX is, we could advise on the option of going direct from Innsbruck.
So where is XXX? Where are you actually trying to get to?

Traveling to Brussels midi station

I guess this is the train you were planning for:

München Hbf dep 11:28, Köln Hbf arr 16:05
Transfer time 38 min.
Köln Hbf dep 16:43, Bruxelles Midi arr 18:35

By train direct from Innsbruck:

Innsbruck Hbf dep 08:38, München-Pasing arr 11:19
Transfer time 17 min.
München-Pasing dep 11:36, Köln Hbf arr 16:05
Transfer time 38 min.
Köln Hbf dep 16:43, Bruxelles Midi arr 18:35

That is exactly the same train Munich - Cologne and Cologne - Brussels.
viaMichelin reckons 1h48 by road from Innsbruck to Munich airport, so the bus must be leaving Innsbruck 07:40 latest.
Train all the way you get an extra hour in bed, and save the leg from Munich airport into Munich Hbf.

The last S-Bahn that will get to your 11:28 train to Cologne is the 10:35.

If your bus is to arrive at Munich airport at 9:30, that means it should be departing Innsbruck about 7:30. You could instead, take the 7:17 EC train to Munich Hbf arriving at 9:02, That will give you plenty of time for breakfast at the station. Suggest a typical beer and a weisswurst, its Munich after all.

The walk up price is 43.80 EUR, but if this is planned for a few weeks from now, you could buy a nonrefundable Sparpreis ticket now for 19.90 EUR. As was stated, the cost of a 1-way ticket from the airport to the Hbf will be 11 EUR and change, so doing this will be a net cost to you of 8 EUR.