I'm looking to identify a book I read in the very early 2000s, it was about a boy who found a dragon egg (I think it was set in England) there was a merlin-type character who helped him and a side character called "Milo"? I barely remember the plot but I think the main character's dad worked at a museum or something.
I hesitate a little to suggest this, as although it matches on some points, it also misses on a few. Could the book be "Pillage" by Obert Skye?
Points in favour:
The boy protagonist, Beck, finds some stone eggs and hatches them into dragons.
He has two friends, one of whom is called Milo.
The story is set in America rather than England (though I think the family is originally from Scotland).
Beck lives with his uncle, rather than his father (his mother and father died I think, leaving him to be brought up by his uncle). But in fact:
it is revealed in a plot-twist near the end, that the man he thought was his uncle was in fact his father.
As @JohnRennie points out, with a publication date of 2008 it's a bit too late to have been read "in the very early 2000s".