I run the entire IT dept., so you'd think I'd be pretty safe.
In your specific case that may be true, but in general I think it isn't. When companies merge, HR and IT departments are often hard hit because of overlap in job responsibilities. This is especially true for smaller companies getting bought by larger companies: you can expect the smaller company's HR and IT departments to virtually disappear.
I've been through it a number of times. The supercomputer center I was at was bought by Cray, who was then bought by SGI... I jumped ship to another company (a large telco) that was bought by an even larger one... Seen it 'nuff times.
That said, every merger is a bit different. So maybe instead of your job being threatened, you'd end up being on the busy end of trying to merge two IT departments.