Henry VII was very aware that in default of his son's line that Margaret's descendants might inherit - he said it didn't matter because the "greater would swallow the smaller" - ie England being richer and more populous would be the dominant partner in any personal union.
Henry VIII's relationship with Margaret's mother was in permanent strain - he continually failed to head her requests for help to retain and regain the regency of Scotland, he preffered instead to listen to both her second and third husbands, failed to understand he reasons for coming to terms with Hamilton (who was seen as pro-french and anti-english), he also ironically believed that her marital traumas were shaming to the whole family. Margaret Tudor was a living example of the adage marry in haste and repent at leisure (something her granddaughter Mary Stuart should have remembered !)
It is hardly surprising that Henry did exclude her descendants from the succession - whilst the young Margaret Douglas was popular with her Uncle her early amorous adventures helped put an end to that and probably contributed to her exclusion from his will. Her eventual marriage was a political one but was seen as a reward to Lennox for his pro-english stance following the death of James V.
Margaret should have at least inherited a portion of her father's estate and she was still making a deal of it decades later.
The Lennox Hamilton rivalry dominates 16th Century Scotland - their claims had nothing to do with unequal marriages many Scots Queen's up to the 16th Century were not of Royal Birth.
Hamilton line:
James II - Mary Stewart married secondly James 1st Lord Hamilton - James Hamilton 1st Earl of Arran - marred 1) Elizabeth Home (divorced 1506 when it was discovered that her first husband was still living) 2) Janet Beaton - James Second Earl of Arran and Duke of Chatelherault. Heir to the throne of Scotland 1542.
Lennox line: James II - Mary Stewart married secondly James 1st Lord Hamilton - Elizabeth Hamilton married Mathew Stewart Earl of Lennox - John 3rd Earl of Lennox - Matthew 4th Earl of Lennox married Lady Margaret Douglas.
The dispute centred on the legality of the 1st Earl of Arran's marriage to Janet Beaton. They were also rivals in the Clydesdale area and Glasgow which made matters worse.
Margaret remained close to Mary Tudor, her cousin throughout her life and indeed she was well treated by her and often given precedent over Elizabeth Tudor during Mary's reign. At Elizabeth's accession she retired from court to her home in Yorkshire - she was an intelligent woman and doted on her sons - in fact many people believe that had Elizabeth allowed her to travel north to join her husband she might have been able to keep Darnley in check.
Darnley in fairness was a teenager when he went North and Mary fell for him - not surprising that at his first taste of real freedom he went off the rails.
Margaret was pretty well treated by Elizabeth, despite her religion, and incarceration in the tower was a bit of an occupational hazard for people of her rank and closeness to the throne and she wasn't above intrigue
