The British and Spanish generally approached New World colonization with very different philosophies. The British settlers who came over aimed to settle permanently in the colonies and build a functioning society. By contrast, the Spanish settlements were usually aimed at extracting resources from the land and its people.

This caused the differences that you've observed because the settlement-oriented British colonies gave people the opportunity to come to the Americas and make a new life for themselves. For a Spaniard, on the other hand, there was no reason to go to New Spain unless they were supervising the extraction operations in place, since the labor was done by native and African slaves. Consequently, many more Europeans emigrated to the British colonies than the Spanish colonies.

Two reasons:

1. The Demographic trough for Native Americans in Mexico (don't have data on further South, but perhaps in many places there too) after the Columbian exchange came 250 years earlier than in the USA and Canada. Probably because the populations were dense enough that the deadly diseases became endemic, rather than recurrently epidemic.

2. At the bottom of the demographic trough for Native Americans in Mexico, they still greatly outnumbered European and African immigrants and mestizos. At the bottom of the trough in Canada and the USA, they were hugely outnumbered. This was due to different immigration and settlement patterns in these countries rather than to different Native American demographics.

Comparison of Native American demographics in Canada, the USA, and Mexico, is interesting, and illustrates the high probability that epidemic diseases were far more responsible for deteriorating Native American demographics than inter cultural violence.

Canada, although not without various forms of racism and oppression of Aboriginal peoples, had a history of much less violence and warfare between settlers and aboriginals than the US.

Although Canadian treatment of Aboriginal peoples was often racist and oppressive to some extent, oppression very rarely was as violent or blatant as in the US, and rarely degenerated into warfare.

http://www.tolerance.cz/courses/papers/hutchin.htm

Nevertheless, the demographic pattern of First Nation populations in Canada was very similar to that in the USA.

There was a catastrophic decrease in Aboriginal population numbers in both countries over several hundred years, leading to a population low point around 1900, since when there has been a considerable population recovery.

The similarity of demographic patterns, despite a considerable difference in the violence of relations, indicates that the main cause of Aboriginal demographic catastrophe in both countries was the impact of recurring epidemic diseases on Aboriginal populations, more than the impact of cross cultural violence.

The First Nations populations of Canada were severely reduced, to a low point around 1900.

In 1900 the First Nation population of Canada was 127,000, or about 2% of a total population of 5,300,000 (of which 5.1m European, 23,000 Asian, 17,000 African, and 127,000 Indigenous).

http://www.chrc-ccdp.ca/en/getBriefed/1900/population.asp

Since 1900, with the arrival of modern medicine, the Aboriginal population of Canada has grown to 1.4 million, and now makes up 4.3% of the population of Canada.

The demographics of American Indian populations in the USA are similar.

http://www.ewi-ssl.pitt.edu/econ/files/courses/110103_misc_nativeamericanpopulationgraphs.pdf

By the time of the first US census (in 1800) the Native American population (in a smaller area than today’s USA, and of dubious accuracy) was enumerated as 600,000. The low point in American Indian population was 1890 at 228,000 (0.4% of the total population of 63m at the time) (Alaskan Natives were included in the “American Indian” category in the 1890 census).

The similar demographic catastrophes for aboriginals in both the US and Canada seem to have been driven primarily by the impact of recurring epidemic diseases.

The low point of the American Indian population in the USA was 1890. Although American Indian populations began to recover after 1890, the American Indian percentage of the population did not start to grow until after 1950, as the non-Indian population (largely through immigration) grew as fast, or faster, than the Indian population.

Since 1950, the American Indian share of the population has grown. By 2010, in the USA, the American Indian and Alaska Native population only identified as such, was 2.9m (0.9% of the population), while those identifying as American Indian or Alaska Native in combination with one or more other groups in the USA was 2.3 million (0.7% of the population). Those identifying as totally or partially American Indian or Alaska Native made up about 1.7% of the population. Between 2000 and 2010, the population of American Indians and Alaska Natives was growing twice as fast as the growth rate of the overall US population, so their percentage of the population is gradually increasing.

http://www.census.gov/prod/cen2010/briefs/c2010br-10.pdf

So, in both the USA and Canada, Native American populations were devastated by recurring epidemic diseases to which they had little immunity. In both countries populations reached a low point about 1900. In both countries, populations have been recovering strongly since then. (In both countries, Native American populations have increased more than tenfold since the demographic low point.)

At the population low point, there were still almost twice as many Native Americans in the USA as in Canada. In 2010 (about 110 years after the low point) there are slightly more than twice as many Native Americans in the USA as in Canada. (The population of Native Americans has been growing faster in the USA than in Canada).

The reason that Native Americans are a lower % of the population in the USA than in Canada is due to the demographics (especially immigration) of the non-Native American populations in those two countries, rather than the demographics of Native Americans. The demographic pattern of aboriginal populations in Mexico was very different.

In Mexico, Indigenous populations also got hammered in a demographic catastrophe by diseases arriving in the Columbian exchange. Estimates vary a lot, but it seems that the bottom of the demographic decline was in the mid 1600s, when the indigenous population in Mexico reached a low point of between 1.2m and 3.4m (down from pre-contact estimates between 5 and 25 m).

Denser Indigenous populations in Mexico may have enabled diseases to become endemic (by about 100 years after the Columbian exchange) instead of remaining epidemic (as they did in much less dense populations in Canada and the USA). Endemic diseases are still deadly, but do not cause such drastic population declines, as they tend to kill off children (the adults being largely survivors who have acquired immunity), and children are more rapidly replaced than adults.

http://www.hist.umn.edu/~rmccaa/mxpoprev/cambridg3.htm

As well as the demographic crash from diseases bottoming much earlier in Mexico (250 years earlier), the numbers of the non-indigenous population, at the time of the low point of the demographic catastrophe in the aboriginal population, were much smaller. In 1650, it is estimated that there were 10,000 Mexicans of European descent, and 35,000 Mexicans of African descent. In addition, there were circa 600,000 Mexicans who were classified as “mestizo” (meaning of mixed Indigenous, European and or African descent) as well as the 1.2m to 3.4m (est.) remaining indigenous population.

With the Indigenous population of Mexico being a much higher proportion of the population at the trough of the demographic crisis, it is not surprising that Mexico should have a much higher percentage of Native Americans in the population today.